Index

_

__init__() (nanobrain.core.a2a_support.A2AAgentCard method) (nanobrain.core.a2a_support.A2AAgentConfig method) (nanobrain.core.a2a_support.A2AArtifact method) (nanobrain.core.a2a_support.A2AAuthentication method) (nanobrain.core.a2a_support.A2ACapabilities method) (nanobrain.core.a2a_support.A2AClient method) (nanobrain.core.a2a_support.A2AClientConfig method) (nanobrain.core.a2a_support.A2AMessage method) (nanobrain.core.a2a_support.A2APart method) (nanobrain.core.a2a_support.A2AProvider method) (nanobrain.core.a2a_support.A2ASkill method) (nanobrain.core.a2a_support.A2ASupportMixin method) (nanobrain.core.a2a_support.A2ATask method) (nanobrain.core.a2a_support.A2ATaskStatus method) (nanobrain.core.a2a_support.MockA2ASession method) (nanobrain.core.agent.AgentLangChainTool method) (nanobrain.core.agent_logging.AgentInteractionLog method) (nanobrain.core.agent_logging.AgentLogger method) (nanobrain.core.AgentConversationLog method), [1] (nanobrain.core.async_logging.LogMessage method) (nanobrain.core.async_logging.ProcessSafeLogger method) (nanobrain.core.bioinformatics.BioinformaticsAgent method) (nanobrain.core.bioinformatics.BioinformaticsDataUnit method) (nanobrain.core.bioinformatics.BioinformaticsStep method) (nanobrain.core.bioinformatics.ExternalToolManager method) (nanobrain.core.BioinformaticsAgent method), [1] (nanobrain.core.BioinformaticsDataUnit method), [1] (nanobrain.core.BioinformaticsStep method), [1] (nanobrain.core.card_schemas.AgentCapabilities method) (nanobrain.core.card_schemas.AgentCard method) (nanobrain.core.card_schemas.CardManager method) (nanobrain.core.card_schemas.IOSchema method) (nanobrain.core.card_schemas.ParameterSchema method) (nanobrain.core.card_schemas.PerformanceMetrics method) (nanobrain.core.card_schemas.Skill method) (nanobrain.core.card_schemas.ToolCard method) (nanobrain.core.card_schemas.UsageExample method) (nanobrain.core.component_base.FromConfigBase method) (nanobrain.core.ConditionalLink method), [1] (nanobrain.core.config.config_base.ConfigBase method) (nanobrain.core.config.config_base.ConfigLoadingContext method) (nanobrain.core.config.config_manager.ConfigManager method) (nanobrain.core.config.config_manager.ProviderConfig method) (nanobrain.core.config.ConfigBase method) (nanobrain.core.config.enhanced_config_manager.EnhancedConfigManager method) (nanobrain.core.config.schema_generator.SchemaGenerator method) (nanobrain.core.config.schema_validator.SchemaValidator method) (nanobrain.core.ConfigLoader method), [1] (nanobrain.core.DirectLink method), [1] (nanobrain.core.ExecutionContext method), [1] (nanobrain.core.external_tool.DiagnosticReport method) (nanobrain.core.external_tool.InstallationStatus method) (nanobrain.core.external_tool.ToolResult method) (nanobrain.core.ExternalToolManager method), [1] (nanobrain.core.FastaParser method), [1] (nanobrain.core.FileLink method), [1] (nanobrain.core.FromConfigBase method), [1] (nanobrain.core.guards.AutoGuardMixin method) (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig method) (nanobrain.core.guards.nanobrain_guard_mixin.AutoGuardMixin method) (nanobrain.core.guards.nanobrain_trigger_guard.TriggerGuardConfig method) (nanobrain.core.guards.NanobrainTriggerGuardConfig method) (nanobrain.core.link.ConditionalLink method) (nanobrain.core.link.DirectLink method) (nanobrain.core.link.FileLink method) (nanobrain.core.link.QueueLink method) (nanobrain.core.link.TransformLink method) (nanobrain.core.logging_system.AgentConversationLog method) (nanobrain.core.logging_system.ExecutionContext method) (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.logging_system.SystemLogManager method) (nanobrain.core.logging_system.ToolCallLog method) (nanobrain.core.mcp_support.MCPClient method) (nanobrain.core.mcp_support.MCPClientConfig method) (nanobrain.core.mcp_support.MCPServerConfig method) (nanobrain.core.mcp_support.MCPSupportMixin method) (nanobrain.core.mcp_support.MCPToolInfo method) (nanobrain.core.NanoBrainLogger method), [1] (nanobrain.core.progressive_scaling.ProgressiveScalingMixin method) (nanobrain.core.prompt_template_manager.PromptTemplateManager method) (nanobrain.core.PromptTemplateManager method), [1] (nanobrain.core.QueueLink method), [1] (nanobrain.core.resource_monitor.DiskSpaceInfo method) (nanobrain.core.resource_monitor.ResourceMonitor method) (nanobrain.core.resource_monitor.ResourceNotification method) (nanobrain.core.sequence_manager.FastaParser method) (nanobrain.core.sequence_manager.SequenceManager method) (nanobrain.core.sequence_manager.SequenceStats method) (nanobrain.core.sequence_manager.SequenceValidator method) (nanobrain.core.SequenceManager method), [1] (nanobrain.core.SequenceStats method), [1] (nanobrain.core.SequenceValidator method), [1] (nanobrain.core.testing.test_constants.TestConstants method) (nanobrain.core.testing.TestConstants method) (nanobrain.core.tool.ToolRegistry method) (nanobrain.core.ToolCallLog method), [1] (nanobrain.core.ToolRegistry method), [1] (nanobrain.core.TransformLink method), [1] (nanobrain.core.workflow.ConfigLoader method) (nanobrain.core.workflow.ProgressReporter method) (nanobrain.core.workflow.ProgressStep method) (nanobrain.core.workflow.WorkflowGraph method) (nanobrain.core.workflow.WorkflowProgress method) (nanobrain.core.WorkflowGraph method), [1] (nanobrain.DirectLink method) (nanobrain.library.agents.CodeWriterAgent method) (nanobrain.library.agents.ConversationalCodeWriterAgent method) (nanobrain.library.agents.ConversationalFileWriterAgent method) (nanobrain.library.agents.enhanced.delegation_engine.DelegationEngine method) (nanobrain.library.agents.enhanced.delegation_engine.DelegationRule method) (nanobrain.library.agents.FileWriterAgent method) (nanobrain.library.agents.specialized.base.SpecializedAgentBase method) (nanobrain.library.agents.specialized.code_writer.CodeWriterAgent method) (nanobrain.library.agents.specialized.code_writer.CodeWriterAgentMixin method) (nanobrain.library.agents.specialized.code_writer.ConversationalCodeWriterAgent method) (nanobrain.library.agents.specialized.CodeWriterAgent method) (nanobrain.library.agents.specialized.ConversationalCodeWriterAgent method) (nanobrain.library.agents.specialized.ConversationalFileWriterAgent method) (nanobrain.library.agents.specialized.file_writer.ConversationalFileWriterAgent method) (nanobrain.library.agents.specialized.file_writer.FileWriterAgent method) (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin method) (nanobrain.library.agents.specialized.FileWriterAgent method) (nanobrain.library.agents.specialized.parsl_agent.ParslAgent method) (nanobrain.library.agents.specialized.ParslAgent method) (nanobrain.library.agents.specialized.protein_synonym_agent.ProteinSynonymAgent method) (nanobrain.library.agents.specialized.ProteinSynonymAgent method) (nanobrain.library.agents.specialized.query_analysis_agent.QueryAnalysisAgent method) (nanobrain.library.agents.specialized.QueryAnalysisAgent method) (nanobrain.library.agents.specialized.SpecializedAgentBase method) (nanobrain.library.agents.SpecializedAgentBase method) (nanobrain.library.ConversationHistoryUnit method), [1] (nanobrain.library.infrastructure.BaseCLI method) (nanobrain.library.infrastructure.CircuitBreaker method) (nanobrain.library.infrastructure.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.AnnotationJobData method) (nanobrain.library.infrastructure.data.cache_manager.CacheManager method) (nanobrain.library.infrastructure.data.CacheManager method) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData method) (nanobrain.library.infrastructure.data.chat_session_data.ChatMessage method) (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData method) (nanobrain.library.infrastructure.data.chat_session_data.ConversationalResponseData method) (nanobrain.library.infrastructure.data.chat_session_data.InteractionMetrics method) (nanobrain.library.infrastructure.data.chat_session_data.QueryClassificationData method) (nanobrain.library.infrastructure.data.ChatMessage method) (nanobrain.library.infrastructure.data.ChatSessionData method) (nanobrain.library.infrastructure.data.conversation_history.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.conversation_history.ConversationMessage method) (nanobrain.library.infrastructure.data.ConversationalResponseData method) (nanobrain.library.infrastructure.data.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.ConversationMessage method) (nanobrain.library.infrastructure.data.data_unit_logger.DataUnitLogger method) (nanobrain.library.infrastructure.data.email_manager.EmailManager method) (nanobrain.library.infrastructure.data.EmailManager method) (nanobrain.library.infrastructure.data.export_manager.ExportManager method) (nanobrain.library.infrastructure.data.ExportManager method) (nanobrain.library.infrastructure.data.QueryClassificationData method) (nanobrain.library.infrastructure.data.session_manager.SessionData method) (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.docker.container_config.ContainerConfig method) (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase method) (nanobrain.library.infrastructure.docker.container_config.DockerComponentBase method) (nanobrain.library.infrastructure.docker.container_config.DockerComponentConfig method) (nanobrain.library.infrastructure.docker.container_config.HealthCheckConfig method) (nanobrain.library.infrastructure.docker.container_config.ResourceLimits method) (nanobrain.library.infrastructure.ExportManager method) (nanobrain.library.infrastructure.InteractiveCLI method) (nanobrain.library.infrastructure.interfaces.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.base_cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig method) (nanobrain.library.infrastructure.interfaces.cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStep method) (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStepConfig method) (nanobrain.library.infrastructure.interfaces.cli.CLICommand method) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig method) (nanobrain.library.infrastructure.interfaces.cli.CLIContext method) (nanobrain.library.infrastructure.interfaces.cli.CLIStep method) (nanobrain.library.infrastructure.interfaces.cli.CLIStepConfig method) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand method) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLIContext method) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.cli.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.cli.FormatterConfig method) (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLI method) (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig method) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLI method) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig method) (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig method) (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressContext method) (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig method) (nanobrain.library.infrastructure.interfaces.cli.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.FormatterConfig method) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.cli.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.CLICommand method) (nanobrain.library.infrastructure.interfaces.CLIConfig method) (nanobrain.library.infrastructure.interfaces.CLIContext method) (nanobrain.library.infrastructure.interfaces.CLIStep method) (nanobrain.library.infrastructure.interfaces.CLIStepConfig method) (nanobrain.library.infrastructure.interfaces.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.database.ConnectionPool method) (nanobrain.library.infrastructure.interfaces.database.DatabaseConfig method) (nanobrain.library.infrastructure.interfaces.database.NoSQLQuery method) (nanobrain.library.infrastructure.interfaces.database.NoSQLResult method) (nanobrain.library.infrastructure.interfaces.database.SQLQuery method) (nanobrain.library.infrastructure.interfaces.database.SQLResult method) (nanobrain.library.infrastructure.interfaces.FormatterConfig method) (nanobrain.library.infrastructure.interfaces.InteractiveCLI method) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig method) (nanobrain.library.infrastructure.interfaces.ProgressConfig method) (nanobrain.library.infrastructure.interfaces.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.ResponseFormatter method) (nanobrain.library.infrastructure.load_balancing.circuit_breaker.CircuitBreaker method) (nanobrain.library.infrastructure.load_balancing.CircuitBreaker method) (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer method) (nanobrain.library.infrastructure.load_balancing.LoadBalancer method) (nanobrain.library.infrastructure.load_balancing.request_queue.QueuedRequest method) (nanobrain.library.infrastructure.load_balancing.request_queue.RequestQueue method) (nanobrain.library.infrastructure.load_balancing.RequestQueue method) (nanobrain.library.infrastructure.LoadBalancer method) (nanobrain.library.infrastructure.monitoring.DiskSpaceInfo method) (nanobrain.library.infrastructure.monitoring.MemoryInfo method) (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMetric method) (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.resource_monitor.DiskSpaceInfo method) (nanobrain.library.infrastructure.monitoring.resource_monitor.MemoryInfo method) (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitor method) (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitorConfig method) (nanobrain.library.infrastructure.monitoring.ResourceMonitor method) (nanobrain.library.infrastructure.monitoring.ResourceMonitorConfig method) (nanobrain.library.infrastructure.ParallelAgentStep method) (nanobrain.library.infrastructure.ParallelConversationalAgentStep method) (nanobrain.library.infrastructure.ParallelStep method) (nanobrain.library.infrastructure.PerformanceMonitor method) (nanobrain.library.infrastructure.RequestQueue method) (nanobrain.library.infrastructure.SessionManager method) (nanobrain.library.infrastructure.steps.AgentRequest method) (nanobrain.library.infrastructure.steps.AgentResponse method) (nanobrain.library.infrastructure.steps.ChatRequest method) (nanobrain.library.infrastructure.steps.ChatResponse method) (nanobrain.library.infrastructure.steps.parallel_agent_step.AgentRequest method) (nanobrain.library.infrastructure.steps.parallel_agent_step.AgentResponse method) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentStep method) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatRequest method) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatResponse method) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentStep method) (nanobrain.library.infrastructure.steps.parallel_step.ParallelStep method) (nanobrain.library.infrastructure.steps.parallel_step.ProcessingRequest method) (nanobrain.library.infrastructure.steps.parallel_step.ProcessingResponse method) (nanobrain.library.infrastructure.steps.parallel_step.ProcessorPool method) (nanobrain.library.infrastructure.steps.ParallelAgentStep method) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentStep method) (nanobrain.library.infrastructure.steps.ParallelStep method) (nanobrain.library.infrastructure.steps.ProcessingRequest method) (nanobrain.library.infrastructure.steps.ProcessingResponse method) (nanobrain.library.infrastructure.steps.ProcessorPool method) (nanobrain.library.interfaces.web.AdaptiveStrategy method) (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifier method) (nanobrain.library.interfaces.web.analysis.IntentClassifier method) (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.api.websocket_router.ConnectionManager method) (nanobrain.library.interfaces.web.api.websocket_router.WebSocketMessage method) (nanobrain.library.interfaces.web.BaseFormatConverter method) (nanobrain.library.interfaces.web.BaseRoutingStrategy method) (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.chatbot_server.ChatbotServer method) (nanobrain.library.interfaces.web.config.web_interface_config.APIConfig method) (nanobrain.library.interfaces.web.config.web_interface_config.ChatConfig method) (nanobrain.library.interfaces.web.config.web_interface_config.CORSConfig method) (nanobrain.library.interfaces.web.config.web_interface_config.LoggingConfig method) (nanobrain.library.interfaces.web.config.web_interface_config.SecurityConfig method) (nanobrain.library.interfaces.web.config.web_interface_config.ServerConfig method) (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig method) (nanobrain.library.interfaces.web.DomainClassifier method) (nanobrain.library.interfaces.web.FormatConverter method) (nanobrain.library.interfaces.web.FormatConverterConfig method) (nanobrain.library.interfaces.web.IntentClassifier method) (nanobrain.library.interfaces.web.middleware.logging_middleware.LoggingMiddleware method) (nanobrain.library.interfaces.web.middleware.LoggingMiddleware method) (nanobrain.library.interfaces.web.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.processing.BaseFormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.BaseFormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverterConfig method) (nanobrain.library.interfaces.web.processing.FormatConverter method) (nanobrain.library.interfaces.web.processing.FormatConverterConfig method) (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandlerConfig method) (nanobrain.library.interfaces.web.processing.streaming_handler.StreamSession method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandlerConfig method) (nanobrain.library.interfaces.web.processing.StreamSession method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.routing.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.BaseRoutingStrategy method) (nanobrain.library.interfaces.web.routing.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.BaseRoutingStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.RoutingStrategyConfig method) (nanobrain.library.interfaces.web.routing.RoutingStrategyConfig method) (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.RoutingStrategyConfig method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory method) (nanobrain.library.interfaces.web.servers.universal_server.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.servers.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory method) (nanobrain.library.interfaces.web.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandlerConfig method) (nanobrain.library.interfaces.web.StreamSession method) (nanobrain.library.interfaces.web.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalServerFactory method) (nanobrain.library.interfaces.web.WebInterfaceConfig method) (nanobrain.library.interfaces.web.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRouter method) (nanobrain.library.interfaces.WebInterfaceConfig method) (nanobrain.library.ParallelAgentStep method), [1] (nanobrain.library.ParallelConversationalAgentStep method), [1] (nanobrain.library.workflows.conversational.viral_expert_workflow.ConversationalResponseFormatter method) (nanobrain.library.workflows.viral_protein_analysis.base_cache_manager.BaseCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.BaseCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.BVBRCCommandPipeline method) (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.CommandResult method) (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineFiles method) (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineResult method) (nanobrain.library.workflows.viral_protein_analysis.steps.alignment_step.AlignmentStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.AlignmentStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.annotation_mapping_step.AnnotationMappingStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.AnnotationMappingStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step.AnnotationData method) (nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step.BVBRCDataAcquisitionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step.GenomeData method) (nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step.ProteinData method) (nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step.SequenceData method) (nanobrain.library.workflows.viral_protein_analysis.steps.BVBRCDataAcquisitionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.clustering_step.ClusteringStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.ClusteringStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step.AnnotationData method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step.BVBRCDataAcquisitionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step.GenomeData method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step.ProteinData method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step.SequenceData method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_aggregation_step.DataAggregationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.DataAggregationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig method) (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.CSVMatchCandidate method) (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.EnhancedBVBRCDataAcquisitionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.ValidationResult method) (nanobrain.library.workflows.viral_protein_analysis.steps.protein_synonym_agent_step.ProteinSynonymAgentStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.ProteinSynonymAgentStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.pssm_analysis_step.PSSMAnalysisStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.PSSMAnalysisStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.result_collection_step.ResultCollectionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.ResultCollectionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.sequence_curation_step.SequenceCurationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.SequenceCurationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.viral_pssm_generation_step.ViralPSSMGenerationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.ViralPSSMGenerationStep method) (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.TaxonInfo method) (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.TaxonResolution method) (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.VirusNameResolver method) (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusCacheEntry method) (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusSpecificCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.VirusSpecificCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.AnalysisProgress method) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneViralProteinInterface method) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.WebSocketManager method) (nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow.WebProgressTracker method) (nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow.WebResultFormatter method) (nanobrain.library.workflows.viral_protein_analysis.web.WebProgressTracker method) (nanobrain.library.workflows.viral_protein_analysis.web.WebResultFormatter method)

_config (nanobrain.core.config.config_manager.ConfigManager attribute) _config_path (nanobrain.core.config.config_manager.ConfigManager attribute) _domain_specific_metrics (nanobrain.library.agents.specialized.base.SpecializedAgentBase attribute) (nanobrain.library.agents.specialized.SpecializedAgentBase attribute) (nanobrain.library.agents.SpecializedAgentBase attribute) _initialize_specialized_features() (nanobrain.library.agents.specialized.base.SpecializedAgentBase method) (nanobrain.library.agents.specialized.SpecializedAgentBase method) (nanobrain.library.agents.SpecializedAgentBase method) _loaded (nanobrain.core.config.config_manager.ConfigManager attribute) _providers (nanobrain.core.config.config_manager.ConfigManager attribute) _registry (nanobrain.core.config.component_factory.ComponentRegistry attribute) _schemas (nanobrain.core.config.schema_generator.SchemaGenerator attribute) _shutdown_specialized_features() (nanobrain.library.agents.specialized.base.SpecializedAgentBase method) (nanobrain.library.agents.specialized.SpecializedAgentBase method) (nanobrain.library.agents.SpecializedAgentBase method) _specialized_errors_count (nanobrain.library.agents.specialized.base.SpecializedAgentBase attribute) (nanobrain.library.agents.specialized.SpecializedAgentBase attribute) (nanobrain.library.agents.SpecializedAgentBase attribute) _specialized_operations_count (nanobrain.library.agents.specialized.base.SpecializedAgentBase attribute) (nanobrain.library.agents.specialized.SpecializedAgentBase attribute) (nanobrain.library.agents.SpecializedAgentBase attribute) _track_specialized_operation() (nanobrain.library.agents.specialized.base.SpecializedAgentBase method) (nanobrain.library.agents.specialized.SpecializedAgentBase method) (nanobrain.library.agents.SpecializedAgentBase method)

A

a2a_agents (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) a2a_client (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) a2a_compatible (nanobrain.core.card_schemas.ToolCard attribute) a2a_config (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent attribute) a2a_config_path (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute), [1] (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute), [1] (nanobrain.library.agents.EnhancedCollaborativeAgent attribute), [1] (nanobrain.library.EnhancedCollaborativeAgent attribute), [1] a2a_support (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.core.bioinformatics.BioinformaticsConfig attribute) (nanobrain.core.config.config_base.ConfigBase attribute) (nanobrain.core.config.ConfigBase attribute) (nanobrain.core.config.yaml_config.YAMLConfig attribute) (nanobrain.core.data_unit.DataUnitConfig attribute) (nanobrain.core.DataUnitConfig attribute), [1] (nanobrain.core.executor.ExecutorConfig attribute) (nanobrain.core.ExecutorConfig attribute), [1] (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig attribute) (nanobrain.core.link.LinkConfig attribute) (nanobrain.core.LinkConfig attribute), [1] (nanobrain.core.prompt_template_manager.PromptTemplateConfig attribute) (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.testing.test_result_config.TestResultConfig attribute) (nanobrain.core.tool.ToolConfig attribute) (nanobrain.core.trigger.TriggerConfig attribute) (nanobrain.core.TriggerConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.request_analyzer.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.analysis.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverterConfig attribute) (nanobrain.library.interfaces.web.processing.FormatConverterConfig attribute) (nanobrain.library.interfaces.web.processing.response_processor.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.processing.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.routing.routing_strategies.RoutingStrategyConfig attribute) (nanobrain.library.interfaces.web.routing.RoutingStrategyConfig attribute) (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.servers.base_server.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.server_factory.ServerFactoryConfig attribute) (nanobrain.library.interfaces.web.servers.ServerFactoryConfig attribute) (nanobrain.library.interfaces.web.servers.universal_server.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.servers.UniversalServerConfig attribute) a2a_version (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.ToolCard attribute) A2AAgentCard (class in nanobrain.core.a2a_support) A2AAgentConfig (class in nanobrain.core.a2a_support) A2AArtifact (class in nanobrain.core.a2a_support) A2AAuthentication (class in nanobrain.core.a2a_support) A2AAuthenticationError A2ACapabilities (class in nanobrain.core.a2a_support) (class in nanobrain.core.config.enhanced_config) A2AClient (class in nanobrain.core.a2a_support) A2AClientConfig (class in nanobrain.core.a2a_support) A2AConfigurationError A2AConnectionError A2AError A2AMessage (class in nanobrain.core.a2a_support) A2APart (class in nanobrain.core.a2a_support) A2AProvider (class in nanobrain.core.a2a_support) A2ASkill (class in nanobrain.core.a2a_support) (class in nanobrain.core.config.enhanced_config) A2ASupportMixin (class in nanobrain.core.a2a_support) A2ATask (class in nanobrain.core.a2a_support) A2ATaskExecutionError A2ATaskStatus (class in nanobrain.core.a2a_support) access_count (nanobrain.core.data_unit.DataUnitBase attribute) (nanobrain.core.DataUnitBase attribute), [1] (nanobrain.library.infrastructure.DataUnitBase attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.WorkflowRegistryEntry attribute) access_log (nanobrain.library.interfaces.web.config.web_interface_config.ServerConfig attribute) active_jobs (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData attribute) (nanobrain.library.infrastructure.data.ChatSessionData attribute) active_workflows (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent attribute) actual_start_time (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) AdaptiveStrategy (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.routing) (class in nanobrain.library.interfaces.web.routing.routing_strategies) add_a2a_agent() (nanobrain.core.a2a_support.A2ASupportMixin method) add_agent() (nanobrain.core.a2a_support.A2AClient method) (nanobrain.core.config.yaml_config.YAMLWorkflowConfig method) add_agent_guards() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_guard_mixin) add_annotation_job() (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData method) (nanobrain.library.infrastructure.data.ChatSessionData method) add_callback() (nanobrain.core.trigger.TriggerBase method) (nanobrain.core.TriggerBase method), [1] add_delegation_rule() (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent method) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent method) (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent method) (nanobrain.library.agents.EnhancedCollaborativeAgent method) (nanobrain.library.EnhancedCollaborativeAgent method), [1] add_event_handler() (nanobrain.library.infrastructure.BaseCLI method) (nanobrain.library.infrastructure.interfaces.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.base_cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.BaseCLI method) add_link() (nanobrain.core.BaseStep method), [1] (nanobrain.core.config.yaml_config.YAMLWorkflowConfig method) (nanobrain.core.step.BaseStep method) (nanobrain.core.workflow.WorkflowGraph method) (nanobrain.core.WorkflowGraph method), [1] add_mcp_server() (nanobrain.core.mcp_support.MCPSupportMixin method) add_message() (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData method) (nanobrain.library.infrastructure.data.ChatSessionData method) add_notification_callback() (nanobrain.core.resource_monitor.ResourceMonitor method) add_processor() (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer method) (nanobrain.library.infrastructure.load_balancing.LoadBalancer method) (nanobrain.library.infrastructure.LoadBalancer method) add_progress_callback() (nanobrain.core.Workflow method), [1] (nanobrain.core.workflow.ProgressReporter method) (nanobrain.core.workflow.Workflow method) add_reference() (nanobrain.library.infrastructure.data.chat_session_data.ConversationalResponseData method) (nanobrain.library.infrastructure.data.ConversationalResponseData method) add_rule() (nanobrain.library.agents.enhanced.delegation_engine.DelegationEngine method) add_server() (nanobrain.core.mcp_support.MCPClient method) add_step() (nanobrain.core.config.yaml_config.YAMLWorkflowConfig method) (nanobrain.core.Workflow method), [1] (nanobrain.core.workflow.Workflow method) (nanobrain.core.workflow.WorkflowGraph method) (nanobrain.core.WorkflowGraph method), [1] add_step_guards() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_guard_mixin) add_template() (nanobrain.library.infrastructure.interfaces.cli.response_formatter.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.cli.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.ResponseFormatter method) add_to_buffer() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamSession method) (nanobrain.library.interfaces.web.processing.StreamSession method) (nanobrain.library.interfaces.web.StreamSession method) add_to_conversation() (nanobrain.core.Agent method), [1] (nanobrain.core.agent.Agent method) add_tool_keywords() (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent method) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent method) (nanobrain.library.agents.EnhancedCollaborativeAgent method) (nanobrain.library.EnhancedCollaborativeAgent method), [1] add_workflow_guards() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_guard_mixin) additional_context (nanobrain.core.config.config_base.ConfigLoadingContext attribute) additional_params (nanobrain.core.config.config_manager.ProviderConfig attribute) advanced_config (nanobrain.library.interfaces.web.routing.routing_strategies.RoutingStrategyConfig attribute) (nanobrain.library.interfaces.web.routing.RoutingStrategyConfig attribute) advanced_patterns (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.IntentClassifierConfig attribute) affinity (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) Agent (class in nanobrain.core), [1] (class in nanobrain.core.agent) agent (nanobrain.core.BaseStep attribute), [1] (nanobrain.core.step.BaseStep attribute) AGENT (nanobrain.core.tool.ToolType attribute) (nanobrain.core.ToolType attribute), [1] agent_card (nanobrain.AgentConfig attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.core.config.enhanced_config.EnhancedAgentConfig attribute), [1] agent_context (nanobrain.library.infrastructure.steps.AgentRequest attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.AgentRequest attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatRequest attribute) agent_implementation (nanobrain.core.config.enhanced_config.EnhancedAgentConfig attribute) agent_initialization_timeout (nanobrain.library.infrastructure.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) agent_metadata (nanobrain.library.infrastructure.steps.AgentResponse attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.AgentResponse attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatResponse attribute) agent_name (nanobrain.core.agent_logging.AgentInteractionLog attribute) (nanobrain.core.AgentConversationLog attribute), [1] (nanobrain.core.logging_system.AgentConversationLog attribute) agent_orchestrator (nanobrain.library.ChatWorkflow attribute), [1] (nanobrain.library.workflows.ChatWorkflow attribute) AGENT_PROCESS (nanobrain.core.logging_system.OperationType attribute) (nanobrain.core.OperationType attribute), [1] agent_response (nanobrain.library.infrastructure.data.conversation_history.ConversationMessage attribute) (nanobrain.library.infrastructure.data.ConversationMessage attribute) agent_shutdown_timeout (nanobrain.library.infrastructure.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) agent_specific_configs (nanobrain.library.infrastructure.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) agent_type (nanobrain.core.agent_logging.AgentInteractionLog attribute) (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.config.enhanced_config.EnhancedAgentConfig attribute) AgentCapabilities (class in nanobrain.core.card_schemas) AgentCard (class in nanobrain.core.card_schemas) AgentCardSection (class in nanobrain.core.config.enhanced_config) AgentConfig (class in nanobrain) (class in nanobrain.core), [1] (class in nanobrain.core.agent) AgentConversationLog (class in nanobrain.core), [1] (class in nanobrain.core.logging_system) AgentInteractionLog (class in nanobrain.core.agent_logging) AgentLangChainTool (class in nanobrain.core.agent) AgentLogger (class in nanobrain.core.agent_logging) AgentRequest (class in nanobrain.library.infrastructure.steps) (class in nanobrain.library.infrastructure.steps.parallel_agent_step)

AgentResponse (class in nanobrain.library.infrastructure.steps) (class in nanobrain.library.infrastructure.steps.parallel_agent_step) agents (nanobrain.core.config.yaml_config.YAMLWorkflowConfig attribute) (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.StepConfig attribute) AgentTool (class in nanobrain.core), [1] (class in nanobrain.core.tool) AgentToolSchema (class in nanobrain.core.agent) aggregated_content (nanobrain.library.interfaces.web.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.AggregatedResponse attribute) AggregatedResponse (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.universal_models) aggregation_id (nanobrain.library.interfaces.web.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.AggregatedResponse attribute) aggregation_method (nanobrain.library.interfaces.web.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.models.universal_models.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.MultiWorkflowRoute attribute) aliases (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) AlignmentStep (class in nanobrain.library.workflows.viral_protein_analysis.steps) (class in nanobrain.library.workflows.viral_protein_analysis.steps.alignment_step) ALL_DATA_RECEIVED (nanobrain.core.trigger.TriggerType attribute) (nanobrain.core.TriggerType attribute), [1] all_genome_names (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.TaxonResolution attribute) AllDataReceivedTrigger (class in nanobrain.core), [1] (class in nanobrain.core.trigger) allow_credentials (nanobrain.library.interfaces.web.config.web_interface_config.CORSConfig attribute) allow_cycles (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] allow_headers (nanobrain.library.interfaces.web.config.web_interface_config.CORSConfig attribute) allow_methods (nanobrain.library.interfaces.web.config.web_interface_config.CORSConfig attribute) allow_origins (nanobrain.library.interfaces.web.config.web_interface_config.CORSConfig attribute) AlphavirusWorkflow (class in nanobrain.library.workflows.viral_protein_analysis) (class in nanobrain.library.workflows.viral_protein_analysis.alphavirus_workflow) alternative_methods (nanobrain.core.external_tool.DiagnosticReport attribute) ALWAYS (nanobrain.library.infrastructure.docker.container_config.RestartPolicy attribute) analysis_depth (nanobrain.library.agents.specialized.query_analysis_agent.QueryAnalysisAgent attribute) (nanobrain.library.agents.specialized.QueryAnalysisAgent attribute) analysis_id (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.AnalysisProgress attribute) analysis_method (nanobrain.library.interfaces.web.analysis.request_analyzer.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.analysis.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.RequestAnalyzerConfig attribute) ANALYSIS_REQUEST (nanobrain.library.interfaces.web.InputType attribute) (nanobrain.library.interfaces.web.IntentType attribute) (nanobrain.library.interfaces.web.models.InputType attribute) (nanobrain.library.interfaces.web.models.IntentType attribute) (nanobrain.library.interfaces.web.models.universal_models.IntentType attribute) (nanobrain.library.interfaces.web.models.workflow_models.InputType attribute) ANALYSIS_RESULTS (nanobrain.library.interfaces.web.models.OutputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.OutputType attribute) (nanobrain.library.interfaces.web.OutputType attribute) analysis_timestamp (nanobrain.library.interfaces.web.models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.models.universal_models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.RequestAnalysis attribute) analysis_type (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.EEEVAnalysisRequest attribute) AnalysisProgress (class in nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface) analyze_request() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) analyze_sequences() (nanobrain.core.bioinformatics.BioinformaticsAgent method) (nanobrain.core.BioinformaticsAgent method), [1] analyzer_metadata (nanobrain.library.interfaces.web.models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.models.universal_models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.RequestAnalysis attribute) ANNOTATION_PROGRESS (nanobrain.library.infrastructure.data.chat_session_data.MessageType attribute) (nanobrain.library.infrastructure.data.MessageType attribute) ANNOTATION_REQUEST (nanobrain.library.infrastructure.data.chat_session_data.MessageType attribute) (nanobrain.library.infrastructure.data.MessageType attribute) annotation_requests (nanobrain.library.infrastructure.data.chat_session_data.InteractionMetrics attribute) ANNOTATION_RESULT (nanobrain.library.infrastructure.data.chat_session_data.MessageType attribute) (nanobrain.library.infrastructure.data.MessageType attribute) AnnotationData (class in nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step) (class in nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step) AnnotationJobData (class in nanobrain.library.infrastructure.data) (class in nanobrain.library.infrastructure.data.chat_session_data) AnnotationMappingStep (class in nanobrain.library.workflows.viral_protein_analysis.steps) (class in nanobrain.library.workflows.viral_protein_analysis.steps.annotation_mapping_step) annotations (nanobrain.core.bioinformatics.SequenceRegion attribute) (nanobrain.core.SequenceRegion attribute), [1] (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) api (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig attribute) (nanobrain.library.interfaces.web.WebInterfaceConfig attribute) (nanobrain.library.interfaces.WebInterfaceConfig attribute) api_client (nanobrain.core.tool.ToolBase attribute) (nanobrain.core.ToolBase attribute), [1] api_key (nanobrain.core.config.config_manager.ProviderConfig attribute) api_status (nanobrain.library.interfaces.web.models.response_models.StatusResponse attribute) api_version (nanobrain.library.interfaces.web.api.frontend_router.SystemInfo attribute) APIConfig (class in nanobrain.library.interfaces.web.config.web_interface_config) APIInterface (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.external) app (nanobrain.library.interfaces.web.web_interface.WebInterface attribute) (nanobrain.library.interfaces.web.WebInterface attribute) (nanobrain.library.interfaces.WebInterface attribute) app_name (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) append (nanobrain.core.a2a_support.A2AArtifact attribute) append() (nanobrain.core.data_unit.DataUnitString method) (nanobrain.core.DataUnitString method), [1] (nanobrain.library.infrastructure.DataUnitString method) append_to_file() (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin method) apply_a2a_integration() (nanobrain.core.config.config_base.ConfigBase method) (nanobrain.core.config.ConfigBase method) apply_compression() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) apply_frontend_optimizations() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) apply_mcp_integration() (nanobrain.core.config.config_base.ConfigBase method) (nanobrain.core.config.ConfigBase method) apply_pagination() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) arg_types (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) args (nanobrain.library.infrastructure.interfaces.cli.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.CLIContext attribute) ARRAY (nanobrain.core.card_schemas.ParameterType attribute) artifacts (nanobrain.core.a2a_support.A2ATask attribute) ASSISTANT (nanobrain.library.infrastructure.data.chat_session_data.MessageRole attribute) (nanobrain.library.infrastructure.data.MessageRole attribute) async_execution (nanobrain.core.tool.ToolBase attribute) (nanobrain.core.tool.ToolConfig attribute) (nanobrain.core.ToolBase attribute), [1] (nanobrain.core.ToolConfig attribute), [1] async_execution_context() (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] async_input (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) AsyncLoggerFactory (class in nanobrain.core.async_logging) audit_trail (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.EnhancedBVBRCDataAcquisitionStep attribute) auth_manager (nanobrain.library.interfaces.web.web_interface.WebInterface attribute) (nanobrain.library.interfaces.web.WebInterface attribute) (nanobrain.library.interfaces.WebInterface attribute) auth_secret_key (nanobrain.library.interfaces.web.config.web_interface_config.SecurityConfig attribute) auth_token (nanobrain.core.a2a_support.A2AAgentConfig attribute) (nanobrain.core.mcp_support.MCPServerConfig attribute) auth_type (nanobrain.core.a2a_support.A2AAgentConfig attribute) (nanobrain.core.mcp_support.MCPServerConfig attribute) authentication (nanobrain.core.a2a_support.A2AAgentCard attribute) (nanobrain.core.card_schemas.AgentCard attribute) authentication_required (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.core.config.enhanced_config.ToolCapabilities attribute) authentication_schemes (nanobrain.core.card_schemas.ToolCard attribute) author (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) AUTO (nanobrain.library.infrastructure.docker.container_config.ContainerOrchestrator attribute) auto_apply (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig attribute) auto_cleanup (nanobrain.library.infrastructure.docker.container_config.DockerComponentConfig attribute) auto_discover_agents (nanobrain.core.a2a_support.A2AClientConfig attribute) auto_discover_tools (nanobrain.core.mcp_support.MCPClientConfig attribute) auto_discover_workflows() (nanobrain.library.interfaces.web.servers.universal_server.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.servers.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.UniversalNanoBrainServer method) auto_discovery (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.WorkflowRegistryConfig attribute) auto_initialize (nanobrain.AgentConfig attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.StepConfig attribute) auto_install() (nanobrain.core.external_tool.ExternalTool method) auto_register_workflows() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) auto_registration (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.WorkflowRegistryConfig attribute) auto_restart_failed_agents (nanobrain.library.infrastructure.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) auto_save_session (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) auto_scaling_enabled (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) auto_start (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIStepConfig attribute) auto_stop (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIStepConfig attribute) AutoGuardMixin (class in nanobrain.core.guards) (class in nanobrain.core.guards.nanobrain_guard_mixin) available_mb (nanobrain.library.infrastructure.monitoring.MemoryInfo attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.MemoryInfo attribute) available_tools (nanobrain.core.Agent property), [1] (nanobrain.core.agent.Agent property) average_response_time (nanobrain.library.infrastructure.data.chat_session_data.InteractionMetrics attribute)

B

backend_job_id (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) backend_url (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) backup_data_unit() (nanobrain.library.infrastructure.data.export_manager.ExportManager method) (nanobrain.library.infrastructure.data.ExportManager method) (nanobrain.library.infrastructure.ExportManager method) BAR (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressStyle attribute) bar_format (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) base_path (nanobrain.core.config.config_base.ConfigLoadingContext attribute) base_url (nanobrain.core.config.config_manager.ProviderConfig attribute) BaseAgent (class in nanobrain.library.agents.specialized.base) BaseCacheManager (class in nanobrain.library.workflows.viral_protein_analysis) (class in nanobrain.library.workflows.viral_protein_analysis.base_cache_manager) BaseCLI (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.cli) (class in nanobrain.library.infrastructure.interfaces.cli.base_cli) BaseFormatConverter (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.processing) (class in nanobrain.library.interfaces.web.processing.format_converter) BaseRoutingStrategy (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.routing) (class in nanobrain.library.interfaces.web.routing.routing_strategies) BaseServerConfig (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.servers) (class in nanobrain.library.interfaces.web.servers.base_server) BaseStep (class in nanobrain.core), [1] (class in nanobrain.core.step) BaseStepCompatibleMeta (class in nanobrain.core.guards) (class in nanobrain.core.guards.nanobrain_enforcer_meta) BaseUniversalServer (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.servers) (class in nanobrain.library.interfaces.web.servers.base_server) BATCH (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIMode attribute) batch_interval (nanobrain.core.workflow.WorkflowProgress attribute) batch_processing (nanobrain.core.config.enhanced_config.ToolCapabilities attribute) (nanobrain.library.infrastructure.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) BATCH_PROCESSING (nanobrain.library.interfaces.web.InteractionPattern attribute) (nanobrain.library.interfaces.web.models.InteractionPattern attribute) (nanobrain.library.interfaces.web.models.workflow_models.InteractionPattern attribute)

batch_processor (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin attribute) BEST_MATCH (nanobrain.library.interfaces.web.models.RoutingStrategy attribute) (nanobrain.library.interfaces.web.models.universal_models.RoutingStrategy attribute) (nanobrain.library.interfaces.web.RoutingStrategy attribute) BestMatchStrategy (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.routing) (class in nanobrain.library.interfaces.web.routing.routing_strategies) BINARY (nanobrain.core.card_schemas.InputMode attribute) (nanobrain.core.card_schemas.OutputMode attribute) bind_action() (nanobrain.core.guards.EnhancedDataUnitChangeTrigger method) (nanobrain.core.guards.trigger_integration.EnhancedDataUnitChangeTrigger method) (nanobrain.core.trigger.DataUnitChangeTrigger method) BIOINFORMATICS (nanobrain.library.interfaces.web.DomainType attribute) (nanobrain.library.interfaces.web.models.DomainType attribute) (nanobrain.library.interfaces.web.models.universal_models.DomainType attribute) BioinformaticsAgent (class in nanobrain.core), [1] (class in nanobrain.core.bioinformatics) BioinformaticsConfig (class in nanobrain.core), [1] (class in nanobrain.core.bioinformatics) BioinformaticsDataUnit (class in nanobrain.core), [1] (class in nanobrain.core.bioinformatics) BioinformaticsStep (class in nanobrain.core), [1] (class in nanobrain.core.bioinformatics) BioinformaticsTool (class in nanobrain.core), [1] (class in nanobrain.core.bioinformatics) biological_context_focus (nanobrain.library.agents.specialized.query_analysis_agent.QueryAnalysisAgent attribute) (nanobrain.library.agents.specialized.QueryAnalysisAgent attribute) biological_validator (nanobrain.library.agents.specialized.query_analysis_agent.QueryAnalysisAgent attribute) (nanobrain.library.agents.specialized.QueryAnalysisAgent attribute) BOOLEAN (nanobrain.core.card_schemas.ParameterType attribute) (nanobrain.core.config.schema_validator.FieldType attribute) broadcast() (nanobrain.library.interfaces.web.api.websocket_router.ConnectionManager method) broadcast_to_all() (in module nanobrain.library.interfaces.web.api.websocket_router) buffer_config (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.processing.StreamingHandlerConfig attribute) buffer_size (nanobrain.core.link.LinkBase attribute) (nanobrain.core.link.LinkConfig attribute) (nanobrain.core.LinkBase attribute), [1] (nanobrain.core.LinkConfig attribute), [1] (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) (nanobrain.LinkConfig attribute) bulk_size (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) bvbrc_tool (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.EnhancedBVBRCDataAcquisitionStep attribute) BVBRCCommandPipeline (class in nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline) BVBRCDataAcquisitionStep (class in nanobrain.library.workflows.viral_protein_analysis.steps) (class in nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step) (class in nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step) (in module nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step)

C

cache (nanobrain.core.tool.ToolBase attribute) (nanobrain.core.ToolBase attribute), [1] cache_analysis() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) cache_execution() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) cache_file() (nanobrain.library.workflows.viral_protein_analysis.base_cache_manager.BaseCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.BaseCacheManager method) cache_manager() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestBVBRCFunctionalityMigration method) (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestCacheStats method) (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestVirusSpecificCacheManagerInheritance method) (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestVirusSpecificOperations method) cache_response() (nanobrain.library.infrastructure.data.cache_manager.CacheManager method) (nanobrain.library.infrastructure.data.CacheManager method) (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) cache_route() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) cache_sequence() (nanobrain.core.sequence_manager.SequenceManager method) (nanobrain.core.SequenceManager method), [1] cache_size (nanobrain.core.data_unit.DataUnitBase attribute) (nanobrain.core.data_unit.DataUnitConfig attribute) (nanobrain.core.DataUnitBase attribute), [1] (nanobrain.core.DataUnitConfig attribute), [1] (nanobrain.DataUnitConfig attribute) (nanobrain.library.infrastructure.DataUnitBase attribute) cache_ttl_seconds (nanobrain.library.infrastructure.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) CacheManager (class in nanobrain.library.infrastructure.data) (class in nanobrain.library.infrastructure.data.cache_manager) caching (nanobrain.core.config.enhanced_config.ToolCapabilities attribute) calculate_adaptive_score() (nanobrain.library.interfaces.web.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.AdaptiveStrategy method) calculate_complexity_handling_score() (nanobrain.library.interfaces.web.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.MultiCriteriaStrategy method) calculate_complexity_score() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) calculate_confidence_score() (nanobrain.library.interfaces.web.routing.routing_strategies.WeightedScoringStrategy method) (nanobrain.library.interfaces.web.routing.WeightedScoringStrategy method) (nanobrain.library.interfaces.web.WeightedScoringStrategy method) calculate_context_weight() (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.DomainClassifier method) calculate_cost_score() (nanobrain.library.interfaces.web.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.MultiCriteriaStrategy method) calculate_domain_match_score() (nanobrain.library.interfaces.web.routing.routing_strategies.WeightedScoringStrategy method) (nanobrain.library.interfaces.web.routing.WeightedScoringStrategy method) (nanobrain.library.interfaces.web.WeightedScoringStrategy method) calculate_intent_match_score() (nanobrain.library.interfaces.web.routing.routing_strategies.WeightedScoringStrategy method) (nanobrain.library.interfaces.web.routing.WeightedScoringStrategy method) (nanobrain.library.interfaces.web.WeightedScoringStrategy method) calculate_multi_criteria_score() (nanobrain.library.interfaces.web.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.MultiCriteriaStrategy method) calculate_overall_progress() (nanobrain.core.workflow.WorkflowProgress method) calculate_reliability_score() (nanobrain.library.interfaces.web.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.MultiCriteriaStrategy method) calculate_selection_score() (nanobrain.library.interfaces.web.AdaptiveStrategy method) (nanobrain.library.interfaces.web.BaseRoutingStrategy method) (nanobrain.library.interfaces.web.BestMatchStrategy method) (nanobrain.library.interfaces.web.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.BaseRoutingStrategy method) (nanobrain.library.interfaces.web.routing.BestMatchStrategy method) (nanobrain.library.interfaces.web.routing.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.BaseRoutingStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.BestMatchStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.WeightedScoringStrategy method) (nanobrain.library.interfaces.web.routing.WeightedScoringStrategy method) (nanobrain.library.interfaces.web.WeightedScoringStrategy method) calculate_stats() (nanobrain.core.sequence_manager.SequenceValidator method) (nanobrain.core.SequenceValidator method), [1] calculate_term_frequency_weight() (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.DomainClassifier method) calculate_workflow_compatibility() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) call() (nanobrain.library.infrastructure.CircuitBreaker method) (nanobrain.library.infrastructure.load_balancing.circuit_breaker.CircuitBreaker method) (nanobrain.library.infrastructure.load_balancing.CircuitBreaker method) call_a2a_agent() (nanobrain.core.a2a_support.A2ASupportMixin method) call_count (nanobrain.core.tool.ToolBase property) (nanobrain.core.ToolBase property), [1] call_mcp_tool() (nanobrain.core.mcp_support.MCPSupportMixin method) call_tool() (nanobrain.core.mcp_support.MCPClient method) callbacks (nanobrain.core.trigger.TriggerBase attribute) (nanobrain.core.TriggerBase attribute), [1] can_execute() (nanobrain.core.executor.ExecutorBase method) (nanobrain.core.ExecutorBase method), [1] cancel_task() (nanobrain.core.a2a_support.A2AClient method) CANCELED (nanobrain.core.a2a_support.TaskStatus attribute) capabilities (nanobrain.core.a2a_support.A2AAgentCard attribute) (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.config.enhanced_config.AgentCardSection attribute) (nanobrain.core.config.enhanced_config.ToolCardSection attribute) (nanobrain.core.mcp_support.MCPServerConfig attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.WorkflowRegistryEntry attribute) capability_alignment (nanobrain.library.interfaces.web.models.universal_models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.WorkflowMatch attribute) capability_detection (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.WorkflowRegistryConfig attribute) CardManager (class in nanobrain.core.card_schemas) case_sensitive_commands (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) categories (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) category (nanobrain.core.async_logging.LogMessage attribute) (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.core.config.enhanced_config.ToolCardSection attribute) (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) change_listeners (nanobrain.core.data_unit.DataUnitBase attribute) (nanobrain.core.DataUnitBase attribute), [1] (nanobrain.library.infrastructure.DataUnitBase attribute) CHAT (nanobrain.library.infrastructure.data.chat_session_data.MessageType attribute) (nanobrain.library.infrastructure.data.MessageType attribute) chat (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig attribute) CHAT (nanobrain.library.interfaces.web.InteractionPattern attribute) (nanobrain.library.interfaces.web.models.InteractionPattern attribute) (nanobrain.library.interfaces.web.models.workflow_models.InteractionPattern attribute) chat (nanobrain.library.interfaces.web.WebInterfaceConfig attribute) (nanobrain.library.interfaces.WebInterfaceConfig attribute) CHAT_REQUEST (nanobrain.library.interfaces.web.api.websocket_router.MessageType attribute) CHAT_RESPONSE (nanobrain.library.interfaces.web.api.websocket_router.MessageType attribute) CHAT_STREAM_CHUNK (nanobrain.library.interfaces.web.api.websocket_router.MessageType attribute) CHAT_STREAM_END (nanobrain.library.interfaces.web.api.websocket_router.MessageType attribute) ChatbotServer (class in nanobrain.library.interfaces.web.chatbot_server) ChatConfig (class in nanobrain.library.interfaces.web.config.web_interface_config) ChatMessage (class in nanobrain.library.infrastructure.data) (class in nanobrain.library.infrastructure.data.chat_session_data) ChatMetadata (class in nanobrain.library.interfaces.web.models.response_models) ChatOptions (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.request_models) ChatRequest (class in nanobrain.library.infrastructure.steps) (class in nanobrain.library.infrastructure.steps.parallel_conversational_agent_step) (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.request_models) ChatResponse (class in nanobrain.library.infrastructure.steps) (class in nanobrain.library.infrastructure.steps.parallel_conversational_agent_step) (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.response_models) ChatSessionData (class in nanobrain.library.infrastructure.data) (class in nanobrain.library.infrastructure.data.chat_session_data) ChatWorkflow (class in nanobrain.library), [1] (class in nanobrain.library.workflows) check_disk_space() (nanobrain.core.resource_monitor.ResourceMonitor method) (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitor method) (nanobrain.library.infrastructure.monitoring.ResourceMonitor method) check_interval (nanobrain.library.infrastructure.docker.container_config.DockerComponentConfig attribute) check_memory_usage() (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitor method) (nanobrain.library.infrastructure.monitoring.ResourceMonitor method) check_rate_limit() (nanobrain.library.infrastructure.data.email_manager.EmailManager method) (nanobrain.library.infrastructure.data.EmailManager method) check_size_limit() (nanobrain.library.interfaces.web.FormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverter method) (nanobrain.library.interfaces.web.processing.FormatConverter method) checkpoint_data (nanobrain.core.workflow.ProgressStep attribute) checks (nanobrain.library.interfaces.web.HealthResponse attribute) (nanobrain.library.interfaces.web.models.HealthResponse attribute) (nanobrain.library.interfaces.web.models.response_models.HealthResponse attribute) chunk (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.StreamingChatResponse attribute) chunk_id (nanobrain.library.interfaces.web.models.StreamingResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StreamingResponse attribute) (nanobrain.library.interfaces.web.StreamingResponse attribute) chunk_type (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.StreamingResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StreamingResponse attribute) (nanobrain.library.interfaces.web.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.StreamingResponse attribute) circuit_breaker_threshold (nanobrain.library.infrastructure.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) CircuitBreaker (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.load_balancing) (class in nanobrain.library.infrastructure.load_balancing.circuit_breaker) CircuitBreakerState (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.load_balancing) (class in nanobrain.library.infrastructure.load_balancing.circuit_breaker) class_field (nanobrain.core.data_unit.DataUnitConfig attribute) (nanobrain.core.DataUnitConfig attribute), [1] (nanobrain.DataUnitConfig attribute) class_path (nanobrain.core.data_unit.DataUnitConfig property) (nanobrain.core.DataUnitConfig property), [1] (nanobrain.DataUnitConfig property) classification_accuracy (nanobrain.library.infrastructure.data.chat_session_data.InteractionMetrics attribute) classification_config (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.DomainClassifierConfig attribute) classification_method (nanobrain.library.interfaces.web.DomainClassification attribute) (nanobrain.library.interfaces.web.IntentClassification attribute) (nanobrain.library.interfaces.web.models.DomainClassification attribute) (nanobrain.library.interfaces.web.models.IntentClassification attribute) (nanobrain.library.interfaces.web.models.universal_models.DomainClassification attribute) (nanobrain.library.interfaces.web.models.universal_models.IntentClassification attribute) classification_time (nanobrain.library.infrastructure.data.chat_session_data.QueryClassificationData attribute) (nanobrain.library.infrastructure.data.QueryClassificationData attribute) classify_domain() (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.DomainClassifier method) classify_domain_hybrid() (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.DomainClassifier method) classify_domain_keyword_based() (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.DomainClassifier method) classify_domain_semantic() (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.DomainClassifier method) classify_intent() (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifier method) (nanobrain.library.interfaces.web.analysis.IntentClassifier method) (nanobrain.library.interfaces.web.IntentClassifier method) classify_intent_hybrid() (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifier method) (nanobrain.library.interfaces.web.analysis.IntentClassifier method) (nanobrain.library.interfaces.web.IntentClassifier method) classify_intent_keyword_based() (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifier method) (nanobrain.library.interfaces.web.analysis.IntentClassifier method) (nanobrain.library.interfaces.web.IntentClassifier method) classify_intent_rule_based() (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifier method) (nanobrain.library.interfaces.web.analysis.IntentClassifier method) (nanobrain.library.interfaces.web.IntentClassifier method) cleanup() (nanobrain.library.infrastructure.interfaces.cli.command_processor.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.cli.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.cli.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.cli.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.ResponseFormatter method) (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineFiles method) (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.protein_synonym_agent_step.ProteinSynonymAgentStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.ProteinSynonymAgentStep method) cleanup_empty_logs() (in module nanobrain.core.logging_system) cleanup_enabled (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitorConfig attribute) (nanobrain.library.infrastructure.monitoring.ResourceMonitorConfig attribute) cleanup_expired_entries() (nanobrain.library.infrastructure.data.cache_manager.CacheManager method) (nanobrain.library.infrastructure.data.CacheManager method) cleanup_expired_streams() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) cleanup_old_exports() (nanobrain.library.infrastructure.data.export_manager.ExportManager method) (nanobrain.library.infrastructure.data.ExportManager method) (nanobrain.library.infrastructure.ExportManager method) cleanup_stream() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) cleanup_temp_file() (nanobrain.core.external_tool.ExternalTool method) cleanup_temp_files (nanobrain.core.bioinformatics.BioinformaticsConfig attribute) (nanobrain.core.BioinformaticsConfig attribute), [1] cleanup_temp_files() (nanobrain.core.bioinformatics.ExternalToolManager method) (nanobrain.core.ExternalToolManager method), [1] clear() (nanobrain.core.bioinformatics.BioinformaticsDataUnit method) (nanobrain.core.BioinformaticsDataUnit method), [1] (nanobrain.core.config.component_factory.ComponentRegistry class method) (nanobrain.core.data_unit.DataUnit method) (nanobrain.core.data_unit.DataUnitBase method) (nanobrain.core.data_unit.DataUnitFile method) (nanobrain.core.data_unit.DataUnitMemory method) (nanobrain.core.data_unit.DataUnitStream method) (nanobrain.core.data_unit.DataUnitString method) (nanobrain.core.DataUnitBase method), [1] (nanobrain.core.DataUnitFile method), [1] (nanobrain.core.DataUnitMemory method), [1] (nanobrain.core.DataUnitStream method), [1] (nanobrain.core.DataUnitString method), [1] (nanobrain.DataUnitMemory method) (nanobrain.library.ConversationHistoryUnit method), [1] (nanobrain.library.DataUnitMemory method), [1] (nanobrain.library.infrastructure.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.conversation_history.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.export_manager.ExportManager method) (nanobrain.library.infrastructure.data.ExportManager method) (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.DataUnitBase method) (nanobrain.library.infrastructure.DataUnitFile method) (nanobrain.library.infrastructure.DataUnitMemory method) (nanobrain.library.infrastructure.DataUnitStream method) (nanobrain.library.infrastructure.DataUnitString method) (nanobrain.library.infrastructure.ExportManager method) (nanobrain.library.infrastructure.load_balancing.request_queue.RequestQueue method) (nanobrain.library.infrastructure.load_balancing.RequestQueue method) (nanobrain.library.infrastructure.RequestQueue method) (nanobrain.library.infrastructure.SessionManager method) clear_cache() (nanobrain.core.ConfigLoader method), [1] (nanobrain.core.sequence_manager.SequenceManager method) (nanobrain.core.SequenceManager method), [1] (nanobrain.core.workflow.ConfigLoader method) (nanobrain.library.workflows.viral_protein_analysis.base_cache_manager.BaseCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.BaseCacheManager method) clear_conversation() (nanobrain.core.Agent method), [1] (nanobrain.core.agent.Agent method) clear_conversation_context() (nanobrain.library.infrastructure.ParallelConversationalAgentStep method) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentStep method) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentStep method) (nanobrain.library.ParallelConversationalAgentStep method), [1] clear_logs() (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] clear_metrics() (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor method) (nanobrain.library.infrastructure.PerformanceMonitor method) clear_response_cache() (nanobrain.library.infrastructure.ParallelConversationalAgentStep method) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentStep method) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentStep method) (nanobrain.library.ParallelConversationalAgentStep method), [1] clear_rules() (nanobrain.library.agents.enhanced.delegation_engine.DelegationEngine method) clear_server_cache() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory method) (nanobrain.library.interfaces.web.UniversalServerFactory method) clear_virus_cache() (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusSpecificCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.VirusSpecificCacheManager method) CLICommand (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.cli) (class in nanobrain.library.infrastructure.interfaces.cli.command_processor) CLIConfig (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.cli) (class in nanobrain.library.infrastructure.interfaces.cli.base_cli) CLIContext (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.cli) (class in nanobrain.library.infrastructure.interfaces.cli.command_processor) client_capabilities (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.StreamingChatRequest attribute) CLIMode (class in nanobrain.library.infrastructure.interfaces.cli.base_cli) CLIStep (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.cli) (class in nanobrain.library.infrastructure.interfaces.cli.cli_step) CLIStepConfig (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.cli) (class in nanobrain.library.infrastructure.interfaces.cli.cli_step) CLITheme (class in nanobrain.library.infrastructure.interfaces.cli.base_cli) close() (nanobrain.core.a2a_support.MockA2ASession method) CLOSED (nanobrain.library.infrastructure.CircuitBreakerState attribute) (nanobrain.library.infrastructure.load_balancing.circuit_breaker.CircuitBreakerState attribute) (nanobrain.library.infrastructure.load_balancing.CircuitBreakerState attribute) CLUSTER_IP (nanobrain.library.infrastructure.docker.container_config.ServiceType attribute) ClusteringStep (class in nanobrain.library.workflows.viral_protein_analysis.steps) (class in nanobrain.library.workflows.viral_protein_analysis.steps.clustering_step) code (nanobrain.core.config.schema_validator.ValidatorFunction attribute) code_keywords (nanobrain.library.agents.specialized.code_writer.CodeWriterAgentMixin attribute) CodeWriterAgent (class in nanobrain.library.agents) (class in nanobrain.library.agents.specialized) (class in nanobrain.library.agents.specialized.code_writer) CodeWriterAgentMixin (class in nanobrain.library.agents.specialized.code_writer) collaboration (nanobrain.core.card_schemas.AgentCapabilities attribute) (nanobrain.core.config.enhanced_config.A2ACapabilities attribute) collaboration_history (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) (nanobrain.library.EnhancedCollaborativeAgent attribute), [1] CollaborativeAgent (class in nanobrain.library.agents.enhanced.collaborative_agent) collapsed_by_default (nanobrain.core.workflow.WorkflowProgress attribute) collect_processing_warnings() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) collect_system_metrics() (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor method) (nanobrain.library.infrastructure.PerformanceMonitor method) collection_interval (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor attribute) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor attribute) (nanobrain.library.infrastructure.PerformanceMonitor attribute) colors (nanobrain.library.infrastructure.interfaces.cli.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.FormatterConfig attribute) command (nanobrain.core.external_tool.ToolResult attribute) (nanobrain.library.infrastructure.docker.container_config.HealthCheckConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.CLIContext attribute) (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.CommandResult attribute) command_prefix (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) command_type (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) CommandProcessor (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.cli) (class in nanobrain.library.infrastructure.interfaces.cli.command_processor) CommandResult (class in nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline) commands_executed (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineResult attribute) CommandType (class in nanobrain.library.infrastructure.interfaces.cli.command_processor) common_use_cases (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.ToolCard attribute) COMPARISON_REQUEST (nanobrain.library.interfaces.web.IntentType attribute) (nanobrain.library.interfaces.web.models.IntentType attribute) (nanobrain.library.interfaces.web.models.universal_models.IntentType attribute) compatibility_reasons (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.WorkflowCompatibilityScore attribute) compile_domain_patterns() (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.DomainClassifier method) compile_intent_patterns() (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifier method) (nanobrain.library.interfaces.web.analysis.IntentClassifier method) (nanobrain.library.interfaces.web.IntentClassifier method) complete_color (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) complete_progress() (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.cli.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.ProgressIndicator method) complete_successfully() (nanobrain.library.infrastructure.data.AnnotationJobData method) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData method) COMPLETED (nanobrain.core.a2a_support.TaskStatus attribute) completed_at (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) complexity (nanobrain.core.card_schemas.Skill attribute) (nanobrain.core.config.enhanced_config.A2ASkill attribute) complexity_score (nanobrain.library.interfaces.web.models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.models.universal_models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.RequestAnalysis attribute) compliance_score (nanobrain.library.interfaces.web.models.workflow_models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.WorkflowValidationResult attribute) component_name (nanobrain.core.async_logging.LogMessage attribute) (nanobrain.core.ExecutionContext attribute), [1] (nanobrain.core.logging_system.ExecutionContext attribute) (nanobrain.library.infrastructure.docker.container_config.DockerComponentConfig attribute) component_scores (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.WorkflowCompatibilityScore attribute) COMPONENT_TYPE (nanobrain.core.Agent attribute), [1] (nanobrain.core.agent.Agent attribute) (nanobrain.core.BaseStep attribute), [1] (nanobrain.core.component_base.FromConfigBase attribute), [1] (nanobrain.core.ConditionalLink attribute), [1] (nanobrain.core.data_unit.DataUnitBase attribute) (nanobrain.core.DataUnitBase attribute), [1] (nanobrain.core.DirectLink attribute), [1] (nanobrain.core.executor.ExecutorBase attribute) (nanobrain.core.ExecutorBase attribute), [1] (nanobrain.core.external_tool.ExternalTool attribute) (nanobrain.core.FromConfigBase attribute), [1], [2], [3] (nanobrain.core.link.ConditionalLink attribute) (nanobrain.core.link.DirectLink attribute) (nanobrain.core.link.LinkBase attribute) (nanobrain.core.LinkBase attribute), [1] (nanobrain.core.step.BaseStep attribute) (nanobrain.core.tool.ToolBase attribute) (nanobrain.core.ToolBase attribute), [1] (nanobrain.core.trigger.TriggerBase attribute) (nanobrain.core.TriggerBase attribute), [1] (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.Workflow attribute) (nanobrain.DirectLink attribute) (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.ConversationalSpecializedAgent attribute) (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.SimpleSpecializedAgent attribute) (nanobrain.library.agents.specialized.base.BaseAgent attribute) (nanobrain.library.agents.specialized.base.ConversationalSpecializedAgent attribute) (nanobrain.library.agents.specialized.base.SimpleSpecializedAgent attribute) (nanobrain.library.agents.specialized.ConversationalSpecializedAgent attribute) (nanobrain.library.agents.specialized.SimpleSpecializedAgent attribute) (nanobrain.library.agents.specialized.virus_extraction_agent.VirusExtractionAgent attribute) (nanobrain.library.agents.specialized.VirusExtractionAgent attribute) (nanobrain.library.ChatWorkflow attribute), [1] (nanobrain.library.EnhancedCollaborativeAgent attribute), [1] (nanobrain.library.infrastructure.DataUnitBase attribute) (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase attribute) (nanobrain.library.infrastructure.docker.container_config.DockerComponentBase attribute) (nanobrain.library.interfaces.web.web_interface.WebInterface attribute) (nanobrain.library.interfaces.web.WebInterface attribute) (nanobrain.library.interfaces.WebInterface attribute) (nanobrain.library.workflows.ChatWorkflow attribute) (nanobrain.library.workflows.ParslChatWorkflow attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.annotation_mapping_step.AnnotationMappingStep attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.AnnotationMappingStep attribute)

ComponentConfigurationError, [1], [2] ComponentDependencyError, [1], [2] ComponentRegistry (class in nanobrain.core.config.component_factory) components (nanobrain.library.interfaces.web.api.frontend_router.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.api.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.BaseServerConfig attribute) (nanobrain.library.interfaces.web.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.servers.base_server.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.universal_server.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.servers.UniversalServerConfig attribute) composition (nanobrain.core.sequence_manager.SequenceStats attribute) (nanobrain.core.SequenceStats attribute), [1] compress_exports() (nanobrain.library.infrastructure.data.export_manager.ExportManager method) (nanobrain.library.infrastructure.data.ExportManager method) (nanobrain.library.infrastructure.ExportManager method) concurrency_limit (nanobrain.core.card_schemas.PerformanceMetrics attribute) concurrency_support (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.config.enhanced_config.PerformanceSpec attribute) concurrent_limit (nanobrain.core.config.enhanced_config.PerformanceSpec attribute) concurrent_requests (nanobrain.core.config.enhanced_config.ToolCapabilities attribute) conda_channel (nanobrain.core.external_tool.ExternalToolConfig attribute) conda_package (nanobrain.core.external_tool.ExternalToolConfig attribute) condition (nanobrain.core.link.LinkBase attribute) (nanobrain.core.link.LinkConfig attribute) (nanobrain.core.LinkBase attribute), [1] (nanobrain.core.LinkConfig attribute), [1] (nanobrain.core.trigger.TriggerBase attribute) (nanobrain.core.trigger.TriggerConfig attribute) CONDITION (nanobrain.core.trigger.TriggerType attribute) condition (nanobrain.core.TriggerBase attribute), [1] (nanobrain.core.TriggerConfig attribute), [1] CONDITION (nanobrain.core.TriggerType attribute), [1] condition (nanobrain.LinkConfig attribute) (nanobrain.TriggerConfig attribute) CONDITIONAL (nanobrain.core.link.LinkType attribute) (nanobrain.core.LinkType attribute), [1] ConditionalLink (class in nanobrain.core), [1] (class in nanobrain.core.link) conditions (nanobrain.library.agents.enhanced.delegation_engine.DelegationRule attribute) confidence (nanobrain.library.infrastructure.data.chat_session_data.ConversationalResponseData attribute) (nanobrain.library.infrastructure.data.chat_session_data.QueryClassificationData attribute) (nanobrain.library.infrastructure.data.ConversationalResponseData attribute) (nanobrain.library.infrastructure.data.QueryClassificationData attribute) (nanobrain.library.interfaces.web.DomainClassification attribute) (nanobrain.library.interfaces.web.IntentClassification attribute) (nanobrain.library.interfaces.web.models.DomainClassification attribute) (nanobrain.library.interfaces.web.models.IntentClassification attribute) (nanobrain.library.interfaces.web.models.universal_models.DomainClassification attribute) (nanobrain.library.interfaces.web.models.universal_models.IntentClassification attribute) (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.TaxonResolution attribute) confidence_score (nanobrain.core.bioinformatics.SequenceRegion attribute) (nanobrain.core.SequenceRegion attribute), [1] (nanobrain.library.interfaces.web.models.response_models.ChatMetadata attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.ValidationResult attribute) confidence_threshold (nanobrain.library.agents.enhanced.delegation_engine.DelegationRule attribute) (nanobrain.library.agents.specialized.query_analysis_agent.QueryAnalysisAgent attribute) (nanobrain.library.agents.specialized.QueryAnalysisAgent attribute) CONFIDENCE_THRESHOLD (nanobrain.library.interfaces.web.models.RoutingStrategy attribute) (nanobrain.library.interfaces.web.models.universal_models.RoutingStrategy attribute) (nanobrain.library.interfaces.web.RoutingStrategy attribute) confidence_thresholds (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.IntentClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.request_analyzer.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.analysis.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.RequestAnalyzerConfig attribute) ConfigBase (class in nanobrain.core.config) (class in nanobrain.core.config.config_base) ConfigLoader (class in nanobrain.core), [1] (class in nanobrain.core.workflow) ConfigLoadingContext (class in nanobrain.core.config.config_base) ConfigManager (class in nanobrain.core.config.config_manager) ConfigSchema (class in nanobrain.core.config.schema_validator) ConfigurableGuardMeta (class in nanobrain.core.guards) (class in nanobrain.core.guards.nanobrain_enforcer_meta) configuration (nanobrain.library.interfaces.web.api.frontend_router.SystemInfo attribute) configuration_status (nanobrain.library.interfaces.web.models.response_models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.WorkflowStatusResponse attribute) ConfigurationManager (class in nanobrain.library.interfaces.web.config) configure_endpoints() (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.universal_server.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.servers.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.UniversalNanoBrainServer method) configure_protocols() (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent method) configure_server_implementation() (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.universal_server.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.servers.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.UniversalNanoBrainServer method) configure_third_party_loggers() (in module nanobrain.core.logging_system) connect() (nanobrain.library.infrastructure.DatabaseInterface method) (nanobrain.library.infrastructure.interfaces.database.DatabaseInterface method) (nanobrain.library.infrastructure.interfaces.DatabaseInterface method) (nanobrain.library.infrastructure.interfaces.external.WebSocketInterface method) (nanobrain.library.infrastructure.interfaces.WebSocketInterface method) (nanobrain.library.interfaces.web.api.websocket_router.ConnectionManager method) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.WebSocketManager method) connect_to_agent() (nanobrain.core.a2a_support.A2AClient method) connect_to_server() (nanobrain.core.mcp_support.MCPClient method) connection_config (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.processing.StreamingHandlerConfig attribute) connection_pool_size (nanobrain.core.a2a_support.A2AClientConfig attribute) (nanobrain.core.mcp_support.MCPClientConfig attribute) connection_timeout (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) ConnectionConfig (class in nanobrain.library.infrastructure.interfaces.database) ConnectionManager (class in nanobrain.library.infrastructure.interfaces.database) (class in nanobrain.library.interfaces.web.api.websocket_router) ConnectionPool (class in nanobrain.library.infrastructure.interfaces.database) connectivity_test (nanobrain.core.external_tool.DiagnosticReport attribute) constraint_type (nanobrain.core.config.schema_validator.FieldConstraint attribute) constraints (nanobrain.core.config.schema_validator.FieldSchema attribute) ConstraintType (class in nanobrain.core.config.schema_validator) contact (nanobrain.core.a2a_support.A2AProvider attribute) ContainerConfig (class in nanobrain.library.infrastructure.docker.container_config) ContainerManagerBase (class in nanobrain.library.infrastructure.docker.container_config) ContainerOrchestrator (class in nanobrain.library.infrastructure.docker.container_config) contains() (nanobrain.core.bioinformatics.SequenceCoordinate method) (nanobrain.core.SequenceCoordinate method), [1] contamination_risk (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.ValidationResult attribute) content (nanobrain.core.prompt_template_manager.PromptTemplate attribute) (nanobrain.core.PromptTemplate attribute), [1] (nanobrain.library.infrastructure.data.chat_session_data.ChatMessage attribute) (nanobrain.library.infrastructure.data.ChatMessage attribute) (nanobrain.library.interfaces.web.models.StreamingResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StreamingResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.UniversalResponse attribute) (nanobrain.library.interfaces.web.StreamingResponse attribute) (nanobrain.library.interfaces.web.UniversalResponse attribute) content_format (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.StreamingChatResponse attribute) content_processing (nanobrain.library.interfaces.web.processing.response_processor.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.ResponseProcessorConfig attribute) content_type (nanobrain.core.card_schemas.IOSchema attribute) content_types (nanobrain.core.config.enhanced_config.InputOutputFormat attribute) context (nanobrain.core.card_schemas.UsageExample attribute) (nanobrain.core.config.enhanced_config.UsageExample attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.AgentRequest attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatRequest attribute) (nanobrain.library.infrastructure.steps.parallel_step.ProcessingRequest attribute) (nanobrain.library.infrastructure.steps.ProcessingRequest attribute) context_retention (nanobrain.core.card_schemas.AgentCapabilities attribute) (nanobrain.core.config.enhanced_config.A2ACapabilities attribute) context_window_size (nanobrain.library.infrastructure.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) contexts (nanobrain.core.prompt_template_manager.PromptTemplateConfig attribute) (nanobrain.core.PromptTemplateConfig attribute), [1] contextvar_protected() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_enforcer_meta) CONTINUE (nanobrain.core.ErrorHandlingStrategy attribute), [1] (nanobrain.core.workflow.ErrorHandlingStrategy attribute) continue_on_error (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) CONVERSATION (nanobrain.library.interfaces.web.DomainType attribute) (nanobrain.library.interfaces.web.models.DomainType attribute) (nanobrain.library.interfaces.web.models.universal_models.DomainType attribute) conversation_history (nanobrain.core.Agent attribute), [1] (nanobrain.core.agent.Agent attribute) conversation_id (nanobrain.library.infrastructure.data.conversation_history.ConversationMessage attribute) (nanobrain.library.infrastructure.data.ConversationMessage attribute) (nanobrain.library.infrastructure.steps.ChatRequest attribute) (nanobrain.library.infrastructure.steps.ChatResponse attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatRequest attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatResponse attribute) (nanobrain.library.interfaces.web.api.frontend_router.ConversationSummary attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendChatRequest attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.api.FrontendChatRequest attribute) (nanobrain.library.interfaces.web.api.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.ChatOptions attribute) (nanobrain.library.interfaces.web.ChatResponse attribute) (nanobrain.library.interfaces.web.FrontendChatRequest attribute) (nanobrain.library.interfaces.web.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.models.ChatOptions attribute) (nanobrain.library.interfaces.web.models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.request_models.ChatOptions attribute) (nanobrain.library.interfaces.web.models.response_models.ChatMetadata attribute) (nanobrain.library.interfaces.web.models.response_models.ChatResponse attribute) conversation_manager (nanobrain.library.ChatWorkflow attribute), [1] (nanobrain.library.workflows.ChatWorkflow attribute) conversation_patterns (nanobrain.core.card_schemas.AgentCard attribute) conversation_timeout_seconds (nanobrain.library.interfaces.web.config.web_interface_config.ChatConfig attribute) CONVERSATIONAL (nanobrain.library.infrastructure.data.chat_session_data.MessageType attribute) (nanobrain.library.infrastructure.data.MessageType attribute) conversational_queries (nanobrain.library.infrastructure.data.chat_session_data.InteractionMetrics attribute) CONVERSATIONAL_QUERY (nanobrain.library.interfaces.web.InputType attribute) (nanobrain.library.interfaces.web.models.InputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.InputType attribute) CONVERSATIONAL_RESPONSE (nanobrain.library.interfaces.web.models.OutputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.OutputType attribute) (nanobrain.library.interfaces.web.OutputType attribute) ConversationalAgent (class in nanobrain) (class in nanobrain.core), [1] (class in nanobrain.core.agent) ConversationalCodeWriterAgent (class in nanobrain.library.agents) (class in nanobrain.library.agents.specialized) (class in nanobrain.library.agents.specialized.code_writer) ConversationalFileWriterAgent (class in nanobrain.library.agents) (class in nanobrain.library.agents.specialized) (class in nanobrain.library.agents.specialized.file_writer) ConversationalResponseData (class in nanobrain.library.infrastructure.data) (class in nanobrain.library.infrastructure.data.chat_session_data) ConversationalResponseFormatter (class in nanobrain.library.workflows.conversational.viral_expert_workflow) ConversationalSpecializedAgent (class in nanobrain.library.agents) (class in nanobrain.library.agents.specialized) (class in nanobrain.library.agents.specialized.base) ConversationHistoryUnit (class in nanobrain.library), [1] (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.data) (class in nanobrain.library.infrastructure.data.conversation_history) ConversationMessage (class in nanobrain.library.infrastructure.data) (class in nanobrain.library.infrastructure.data.conversation_history) ConversationSummary (class in nanobrain.library.interfaces.web.api.frontend_router) conversion_config (nanobrain.library.interfaces.web.processing.format_converter.FormatConverterConfig attribute) (nanobrain.library.interfaces.web.processing.FormatConverterConfig attribute) convert() (nanobrain.library.interfaces.web.BaseFormatConverter method) (nanobrain.library.interfaces.web.CSVConverter method) (nanobrain.library.interfaces.web.JSONConverter method) (nanobrain.library.interfaces.web.processing.BaseFormatConverter method) (nanobrain.library.interfaces.web.processing.CSVConverter method) (nanobrain.library.interfaces.web.processing.format_converter.BaseFormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.CSVConverter method) (nanobrain.library.interfaces.web.processing.format_converter.JSONConverter method) (nanobrain.library.interfaces.web.processing.format_converter.TextConverter method) (nanobrain.library.interfaces.web.processing.JSONConverter method) (nanobrain.library.interfaces.web.processing.TextConverter method) (nanobrain.library.interfaces.web.TextConverter method) convert_execution_strategy() (nanobrain.core.workflow.WorkflowConfig class method) (nanobrain.core.WorkflowConfig class method), [1] convert_format() (nanobrain.library.interfaces.web.FormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverter method) (nanobrain.library.interfaces.web.processing.FormatConverter method) convert_to_chat_response() (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) convert_to_universal_format() (nanobrain.library.interfaces.web.FormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverter method) (nanobrain.library.interfaces.web.processing.FormatConverter method) convert_universal_request_to_workflow_format() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) convert_workflow_result_to_universal_response() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) coordinate_system (nanobrain.core.bioinformatics.BioinformaticsConfig attribute) (nanobrain.core.bioinformatics.SequenceCoordinate attribute) (nanobrain.core.BioinformaticsConfig attribute), [1] (nanobrain.core.SequenceCoordinate attribute), [1] coordinates (nanobrain.core.bioinformatics.SequenceRegion attribute) (nanobrain.core.SequenceRegion attribute), [1] CoordinateSystem (class in nanobrain.core), [1] (class in nanobrain.core.bioinformatics) core_workflow (nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow.ViralAnalysisWebWorkflow attribute) (nanobrain.library.workflows.viral_protein_analysis.web.ViralAnalysisWebWorkflow attribute) cors (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig attribute) (nanobrain.library.interfaces.web.WebInterfaceConfig attribute) (nanobrain.library.interfaces.WebInterfaceConfig attribute) cors_config (nanobrain.library.interfaces.web.servers.universal_server.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.servers.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.UniversalServerConfig attribute) cors_enabled (nanobrain.library.interfaces.web.config.web_interface_config.SecurityConfig attribute) CORSConfig (class in nanobrain.library.interfaces.web.config.web_interface_config) COUNTER (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressStyle attribute) cpu (nanobrain.library.infrastructure.docker.container_config.ResourceLimits attribute) cpu_period (nanobrain.library.infrastructure.docker.container_config.ResourceLimits attribute) cpu_quota (nanobrain.library.infrastructure.docker.container_config.ResourceLimits attribute) cpu_request (nanobrain.library.infrastructure.docker.container_config.ResourceLimits attribute) cpu_requirements (nanobrain.core.card_schemas.PerformanceMetrics attribute) (nanobrain.core.config.enhanced_config.PerformanceSpec attribute) create_a2a_agent_config() (in module nanobrain.core.a2a_support) create_agent() (in module nanobrain.core), [1] (in module nanobrain.core.agent) create_agent_config_template() (in module nanobrain.core.config.enhanced_config) create_agent_guard_config() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_guard_config) create_agent_logger() (in module nanobrain.core.agent_logging) create_app() (in module nanobrain.library.interfaces.web.web_interface) (in module nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface) create_bioinformatics_data_unit() (in module nanobrain.core), [1] (in module nanobrain.core.bioinformatics) create_chat_workflow() (in module nanobrain.library.workflows) create_cli_step() (in module nanobrain.library.infrastructure.interfaces.cli.cli_step) create_command() (in module nanobrain.library.infrastructure.interfaces.cli.command_processor) create_component() (in module nanobrain.core.config.component_factory) create_container() (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase method) create_default() (nanobrain.library.interfaces.web.web_interface.WebInterface class method) (nanobrain.library.interfaces.web.WebInterface class method) (nanobrain.library.interfaces.WebInterface class method) create_directory() (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin method) create_error_response() (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.WorkflowRouter method) create_error_route() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) create_example_config() (in module nanobrain.core.config.yaml_config) create_executor() (in module nanobrain.core), [1] (in module nanobrain.core.executor) create_fallback_analysis() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) create_fallback_classification() (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifier method) (nanobrain.library.interfaces.web.analysis.IntentClassifier method) (nanobrain.library.interfaces.web.DomainClassifier method) (nanobrain.library.interfaces.web.IntentClassifier method) create_fallback_route() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) create_fasta_parser() (in module nanobrain.core), [1] (in module nanobrain.core.sequence_manager) create_fastapi_server() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory class method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory class method) (nanobrain.library.interfaces.web.UniversalServerFactory class method) create_flask_server() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory class method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory class method) (nanobrain.library.interfaces.web.UniversalServerFactory class method) create_formatter() (in module nanobrain.library.infrastructure.interfaces.cli.response_formatter) create_guard_aware_trigger() (in module nanobrain.core.guards) (in module nanobrain.core.guards.trigger_integration) create_instance() (nanobrain.core.component_base.FromConfigBase class method) (nanobrain.core.FromConfigBase class method), [1] create_interactive_cli() (in module nanobrain.library.infrastructure.interfaces.cli.interactive_cli) create_isolated_environment (nanobrain.core.external_tool.ExternalToolConfig attribute) create_langchain_agent_executor() (in module nanobrain.core.agent) create_mcp_server_config() (in module nanobrain.core.mcp_support) create_oauth_a2a_agent_config() (in module nanobrain.core.a2a_support) create_oauth_mcp_server_config() (in module nanobrain.core.mcp_support) create_parsl_chat_workflow() (in module nanobrain.library.workflows) create_progress() (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.cli.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.ProgressIndicator method) create_progress_indicator() (in module nanobrain.library.infrastructure.interfaces.cli.progress_indicator) create_protected_step_from_existing() (in module nanobrain.core.guards.examples.protected_step_example) create_protected_step_with_config() (in module nanobrain.core.guards.examples.protected_step_example) create_schema_from_yaml() (in module nanobrain.core.config.schema_validator) create_scope_guard() (nanobrain.core.guards.nanobrain_trigger_guard.NanobrainTriggerGuard class method) (nanobrain.core.guards.NanobrainTriggerGuard class method) create_sequence_coordinate() (in module nanobrain.core), [1] (in module nanobrain.core.bioinformatics) create_sequence_manager() (in module nanobrain.core), [1] (in module nanobrain.core.sequence_manager) create_sequence_region() (in module nanobrain.core), [1] (in module nanobrain.core.bioinformatics) create_sequence_validator() (in module nanobrain.core), [1] (in module nanobrain.core.sequence_manager) create_server() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory class method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory class method) (nanobrain.library.interfaces.web.UniversalServerFactory class method) create_server_from_template() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory class method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory class method) (nanobrain.library.interfaces.web.UniversalServerFactory class method) create_server_with_caching() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory method) (nanobrain.library.interfaces.web.UniversalServerFactory method) create_session() (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.SessionManager method) create_session_summary() (in module nanobrain.core.logging_system) (nanobrain.core.logging_system.SystemLogManager method) (nanobrain.library.infrastructure.data.data_unit_logger.DataUnitLogger method) create_specialized_agent() (in module nanobrain.library.agents) (in module nanobrain.library.agents.specialized) (in module nanobrain.library.agents.specialized.base) create_step_guard_config() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_guard_config) create_stream() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) create_system_command() (in module nanobrain.library.infrastructure.interfaces.cli.command_processor) create_temp_file() (nanobrain.core.bioinformatics.ExternalToolManager method) (nanobrain.core.external_tool.ExternalTool method) (nanobrain.core.ExternalToolManager method), [1] create_tool() (in module nanobrain.core), [1] (in module nanobrain.core.tool) create_tool_config_template() (in module nanobrain.core.config.enhanced_config) create_web_interface() (in module nanobrain.library.interfaces.web.web_interface) create_workflow() (in module nanobrain.core), [1] (in module nanobrain.core.workflow) create_workflow_error_response() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) create_workflow_guard_config() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_guard_config) created_at (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData attribute) (nanobrain.library.infrastructure.data.ChatSessionData attribute) (nanobrain.library.infrastructure.data.session_manager.SessionData attribute) (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusCacheEntry attribute) created_date (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) CRITICAL (nanobrain.core.logging_system.LogLevel attribute) (nanobrain.core.LogLevel attribute), [1] critical() (nanobrain.core.async_logging.ProcessSafeLogger method) (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] critical_triggered (nanobrain.core.resource_monitor.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.MemoryInfo attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.MemoryInfo attribute) CSVConverter (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.processing) (class in nanobrain.library.interfaces.web.processing.format_converter) CSVMatchCandidate (class in nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step) current_step (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.AnalysisProgress attribute) current_step_index (nanobrain.core.workflow.WorkflowProgress attribute) custom_commands (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) custom_formatter (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) custom_metrics (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor attribute) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor attribute) (nanobrain.library.infrastructure.PerformanceMonitor attribute) custom_prompt_function (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) custom_settings (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig attribute) (nanobrain.library.interfaces.web.WebInterfaceConfig attribute) (nanobrain.library.interfaces.WebInterfaceConfig attribute)

D

DARK (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLITheme attribute) data (nanobrain.core.a2a_support.A2APart attribute) DATA (nanobrain.core.a2a_support.PartType attribute) (nanobrain.core.card_schemas.InputMode attribute) (nanobrain.core.card_schemas.OutputMode attribute) data (nanobrain.core.data_unit.DataUnitBase attribute) (nanobrain.core.DataUnitBase attribute), [1] (nanobrain.library.infrastructure.data.session_manager.SessionData attribute) (nanobrain.library.infrastructure.DataUnitBase attribute) (nanobrain.library.interfaces.web.api.websocket_router.WebSocketMessage attribute) (nanobrain.library.interfaces.web.models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.StandardizedResponse attribute) DATA_CHUNKS (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingType attribute) (nanobrain.library.interfaces.web.processing.StreamingType attribute) (nanobrain.library.interfaces.web.StreamingType attribute) data_mapping (nanobrain.core.link.LinkConfig attribute) (nanobrain.core.LinkConfig attribute), [1] (nanobrain.LinkConfig attribute) DATA_TRANSFER (nanobrain.core.logging_system.OperationType attribute) (nanobrain.core.OperationType attribute), [1] data_type (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusCacheEntry attribute) data_units (nanobrain.core.config.yaml_config.YAMLWorkflowConfig attribute) DATA_UPDATED (nanobrain.core.trigger.TriggerType attribute) (nanobrain.core.TriggerType attribute), [1] DATA_UPLOAD (nanobrain.library.interfaces.web.InteractionPattern attribute) (nanobrain.library.interfaces.web.models.InteractionPattern attribute) (nanobrain.library.interfaces.web.models.workflow_models.InteractionPattern attribute) DataAggregationStep (class in nanobrain.library.workflows.viral_protein_analysis.steps) (class in nanobrain.library.workflows.viral_protein_analysis.steps.data_aggregation_step) database (nanobrain.library.infrastructure.interfaces.database.DatabaseConfig attribute) (nanobrain.library.infrastructure.interfaces.database.SQLiteConfig attribute) DatabaseConfig (class in nanobrain.library.infrastructure.interfaces.database) DatabaseInterface (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.database) DataUnit (class in nanobrain.core.data_unit) DataUnitBase (class in nanobrain.core), [1] (class in nanobrain.core.data_unit) (class in nanobrain.library.infrastructure) DataUnitChangeTrigger (class in nanobrain.core.trigger) DataUnitConfig (class in nanobrain) (class in nanobrain.core), [1] (class in nanobrain.core.data_unit) DataUnitFile (class in nanobrain.core), [1] (class in nanobrain.core.data_unit) (class in nanobrain.library.infrastructure) DataUnitLogger (class in nanobrain.library.infrastructure.data.data_unit_logger) DataUnitMemory (class in nanobrain) (class in nanobrain.core), [1] (class in nanobrain.core.data_unit) (class in nanobrain.library), [1] (class in nanobrain.library.infrastructure) DataUnitStream (class in nanobrain.core), [1] (class in nanobrain.core.data_unit) (class in nanobrain.library.infrastructure) DataUnitString (class in nanobrain.core), [1] (class in nanobrain.core.data_unit) (class in nanobrain.library.infrastructure) DataUpdatedTrigger (class in nanobrain) (class in nanobrain.core), [1] (class in nanobrain.core.trigger) debounce_ms (nanobrain.core.trigger.TriggerBase attribute) (nanobrain.core.trigger.TriggerConfig attribute) (nanobrain.core.TriggerBase attribute), [1] (nanobrain.core.TriggerConfig attribute), [1] (nanobrain.TriggerConfig attribute) DEBUG (nanobrain.core.logging_system.LogLevel attribute) (nanobrain.core.LogLevel attribute), [1] (nanobrain.library.infrastructure.interfaces.cli.response_formatter.MessageType attribute) debug (nanobrain.library.interfaces.web.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.base_server.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.universal_server.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.servers.UniversalServerConfig attribute) debug() (nanobrain.core.async_logging.ProcessSafeLogger method) (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] debug_mode (nanobrain.AgentConfig attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig attribute) (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.StepConfig attribute) deduplicate_requests() (nanobrain.library.infrastructure.data.cache_manager.CacheManager method) (nanobrain.library.infrastructure.data.CacheManager method) default (nanobrain.core.card_schemas.ParameterSchema attribute) (nanobrain.core.config.schema_validator.FieldSchema attribute) DEFAULT (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLITheme attribute) default_format (nanobrain.library.infrastructure.interfaces.cli.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.FormatterConfig attribute) default_input_modes (nanobrain.core.card_schemas.AgentCard attribute) default_max_retries (nanobrain.core.a2a_support.A2AClientConfig attribute) (nanobrain.core.mcp_support.MCPClientConfig attribute) default_max_tokens (nanobrain.library.interfaces.web.config.web_interface_config.ChatConfig attribute) default_organism (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneConfig attribute) default_output_modes (nanobrain.core.card_schemas.AgentCard attribute) default_retry_delay (nanobrain.core.a2a_support.A2AClientConfig attribute) (nanobrain.core.mcp_support.MCPClientConfig attribute) default_server_type (nanobrain.library.interfaces.web.ServerFactoryConfig attribute) (nanobrain.library.interfaces.web.servers.server_factory.ServerFactoryConfig attribute) (nanobrain.library.interfaces.web.servers.ServerFactoryConfig attribute) default_temperature (nanobrain.library.interfaces.web.config.web_interface_config.ChatConfig attribute) default_timeout (nanobrain.core.a2a_support.A2AClientConfig attribute) (nanobrain.core.mcp_support.MCPClientConfig attribute) default_use_rag (nanobrain.library.interfaces.web.config.web_interface_config.ChatConfig attribute) defaultInputModes (nanobrain.core.a2a_support.A2AAgentCard attribute) defaultOutputModes (nanobrain.core.a2a_support.A2AAgentCard attribute) delegation (nanobrain.core.card_schemas.AgentCapabilities attribute) (nanobrain.core.config.enhanced_config.A2ACapabilities attribute) delegation_count (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) (nanobrain.library.EnhancedCollaborativeAgent attribute), [1] delegation_engine (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent attribute) delegation_rules (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) (nanobrain.library.EnhancedCollaborativeAgent attribute), [1] DelegationEngine (class in nanobrain.library.agents.enhanced.delegation_engine) DelegationRule (class in nanobrain.library.agents.enhanced.delegation_engine) delete_conversation() (in module nanobrain.library.interfaces.web.api.chat_router) (in module nanobrain.library.interfaces.web.api.frontend_router) delete_file() (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin method) delete_session() (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.SessionManager method) dependencies (nanobrain.core.card_schemas.Skill attribute) (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.WorkflowExecutionPlan attribute) dependencies_status (nanobrain.library.interfaces.web.models.response_models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.WorkflowStatusResponse attribute) dependency_status (nanobrain.core.external_tool.DiagnosticReport attribute) deprecated (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) description (nanobrain.AgentConfig attribute) (nanobrain.core.a2a_support.A2AAgentCard attribute) (nanobrain.core.a2a_support.A2AAgentConfig attribute) (nanobrain.core.a2a_support.A2AArtifact attribute) (nanobrain.core.a2a_support.A2ASkill attribute) (nanobrain.core.Agent attribute), [1] (nanobrain.core.agent.Agent attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.core.BaseStep attribute), [1] (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.IOSchema attribute) (nanobrain.core.card_schemas.ParameterSchema attribute) (nanobrain.core.card_schemas.Skill attribute) (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.core.card_schemas.UsageExample attribute) (nanobrain.core.config.enhanced_config.A2ASkill attribute) (nanobrain.core.config.enhanced_config.EnhancedAgentConfig attribute) (nanobrain.core.config.enhanced_config.EnhancedToolConfig attribute) (nanobrain.core.config.enhanced_config.UsageExample attribute) (nanobrain.core.config.schema_validator.ConfigSchema attribute) (nanobrain.core.config.schema_validator.FieldSchema attribute) (nanobrain.core.config.schema_validator.ParameterSchema attribute) (nanobrain.core.config.schema_validator.ValidatorFunction attribute) (nanobrain.core.config.yaml_config.YAMLWorkflowConfig attribute) (nanobrain.core.data_unit.DataUnitConfig attribute) (nanobrain.core.DataUnitConfig attribute), [1] (nanobrain.core.mcp_support.MCPServerConfig attribute) (nanobrain.core.mcp_support.MCPToolInfo attribute) (nanobrain.core.prompt_template_manager.PromptTemplate attribute) (nanobrain.core.prompt_template_manager.PromptTemplateConfig attribute) (nanobrain.core.PromptTemplate attribute), [1] (nanobrain.core.PromptTemplateConfig attribute), [1] (nanobrain.core.step.BaseStep attribute) (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.testing.test_result_config.TestResultConfig attribute) (nanobrain.core.testing.TestResultConfig attribute) (nanobrain.core.tool.ToolBase attribute) (nanobrain.core.tool.ToolConfig attribute) (nanobrain.core.ToolBase attribute), [1] (nanobrain.core.ToolConfig attribute), [1] (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.ProgressStep attribute) (nanobrain.core.workflow.Workflow attribute) (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.DataUnitConfig attribute) (nanobrain.library.agents.enhanced.delegation_engine.DelegationRule attribute) (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.library.interfaces.web.config.web_interface_config.APIConfig attribute) (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WebInterfaceConfig attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) (nanobrain.library.interfaces.WebInterfaceConfig attribute) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneConfig attribute) (nanobrain.StepConfig attribute)

detailed_description (nanobrain.core.config.enhanced_config.AgentCardSection attribute) (nanobrain.core.config.enhanced_config.ToolCardSection attribute) detailed_diagnostics (nanobrain.core.external_tool.ExternalToolConfig attribute) details (nanobrain.library.interfaces.web.ErrorResponse attribute) (nanobrain.library.interfaces.web.models.ErrorResponse attribute) (nanobrain.library.interfaces.web.models.response_models.ErrorResponse attribute) detect_categories() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) detect_content_format() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) detect_domains() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) detect_existing_installation() (nanobrain.core.external_tool.ExternalTool method) detect_input_types() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) detect_interaction_patterns() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) detect_natural_language_input() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) detect_output_types() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) detect_response_format() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) DiagnosticReport (class in nanobrain.core.external_tool) DICT (nanobrain.core.config.schema_validator.FieldType attribute) DIRECT (nanobrain.core.link.LinkType attribute) (nanobrain.core.LinkType attribute), [1] DirectLink (class in nanobrain) (class in nanobrain.core), [1] (class in nanobrain.core.link) disable_rule() (nanobrain.library.agents.enhanced.delegation_engine.DelegationEngine method) disconnect() (nanobrain.library.infrastructure.DatabaseInterface method) (nanobrain.library.infrastructure.interfaces.database.DatabaseInterface method) (nanobrain.library.infrastructure.interfaces.DatabaseInterface method) (nanobrain.library.interfaces.web.api.websocket_router.ConnectionManager method) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.WebSocketManager method) discover_agent_capabilities() (nanobrain.core.a2a_support.A2AClient method) discover_agent_configs() (nanobrain.core.config.enhanced_config_manager.EnhancedConfigManager method), [1] discover_cards() (nanobrain.core.card_schemas.CardManager method) discover_tool_configs() (nanobrain.core.config.enhanced_config_manager.EnhancedConfigManager method), [1] discover_tools() (nanobrain.core.mcp_support.MCPClient method) discover_workflows() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) discover_workflows_in_path() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) discovered_workflows (nanobrain.library.interfaces.web.models.workflow_models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.WorkflowDiscoveryResult attribute) discovery_id (nanobrain.library.interfaces.web.models.workflow_models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.WorkflowDiscoveryResult attribute) discovery_metadata (nanobrain.library.interfaces.web.models.workflow_models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.WorkflowDiscoveryResult attribute) discovery_method (nanobrain.library.interfaces.web.models.workflow_models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.WorkflowDiscoveryResult attribute) discovery_paths (nanobrain.library.interfaces.web.models.workflow_models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.WorkflowRegistryConfig attribute) disk_critical_gb (nanobrain.core.resource_monitor.ResourceMonitorConfig attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitorConfig attribute) (nanobrain.library.infrastructure.monitoring.ResourceMonitorConfig attribute) disk_warning_gb (nanobrain.core.resource_monitor.ResourceMonitorConfig attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitorConfig attribute) (nanobrain.library.infrastructure.monitoring.ResourceMonitorConfig attribute) DiskSpaceInfo (class in nanobrain.core.resource_monitor) (class in nanobrain.library.infrastructure.monitoring) (class in nanobrain.library.infrastructure.monitoring.resource_monitor) dispatch() (nanobrain.library.interfaces.web.middleware.logging_middleware.LoggingMiddleware method) (nanobrain.library.interfaces.web.middleware.LoggingMiddleware method) DNA (nanobrain.core.bioinformatics.SequenceType attribute) (nanobrain.core.SequenceType attribute), [1] DNA_CHARS (nanobrain.core.sequence_manager.SequenceValidator attribute) (nanobrain.core.SequenceValidator attribute), [1] DNA_SEQUENCE (nanobrain.library.interfaces.web.InputType attribute) (nanobrain.library.interfaces.web.models.InputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.InputType attribute) DOCKER (nanobrain.library.infrastructure.docker.container_config.ContainerOrchestrator attribute) docker_client (nanobrain.library.infrastructure.docker.container_config.DockerComponentConfig attribute) DOCKER_COMPOSE (nanobrain.library.infrastructure.docker.container_config.ContainerOrchestrator attribute) DOCKER_SWARM (nanobrain.library.infrastructure.docker.container_config.ContainerOrchestrator attribute) DockerComponentBase (class in nanobrain.library.infrastructure.docker.container_config) DockerComponentConfig (class in nanobrain.library.infrastructure.docker.container_config) docs_url (nanobrain.library.interfaces.web.config.web_interface_config.APIConfig attribute) documentation_url (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.ToolCard attribute) documentationUrl (nanobrain.core.a2a_support.A2AAgentCard attribute) domain (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.config.enhanced_config.AgentCardSection attribute) domain_classification (nanobrain.library.interfaces.web.models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.models.universal_models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.RequestAnalysis attribute) domain_classifier (nanobrain.library.interfaces.web.analysis.request_analyzer.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.analysis.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.RequestAnalyzerConfig attribute) domain_patterns (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.DomainClassifierConfig attribute) domain_type (nanobrain.library.interfaces.web.DomainClassification attribute) (nanobrain.library.interfaces.web.models.DomainClassification attribute) (nanobrain.library.interfaces.web.models.universal_models.DomainClassification attribute) DomainClassification (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.universal_models) DomainClassifier (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.analysis) (class in nanobrain.library.interfaces.web.analysis.domain_classifier) DomainClassifierConfig (class in nanobrain.library.interfaces.web.analysis) (class in nanobrain.library.interfaces.web.analysis.domain_classifier) domains (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) DomainType (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.universal_models) DOTS (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressStyle attribute) duration_ms (nanobrain.core.agent_logging.AgentInteractionLog attribute) (nanobrain.core.AgentConversationLog attribute), [1] (nanobrain.core.ExecutionContext attribute), [1] (nanobrain.core.logging_system.AgentConversationLog attribute) (nanobrain.core.logging_system.ExecutionContext attribute) (nanobrain.core.logging_system.ToolCallLog attribute) (nanobrain.core.ToolCallLog attribute), [1]

E

EEEVAnalysisRequest (class in nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface) elapsed_time (nanobrain.core.workflow.ProgressStep attribute) ElasticsearchIndexingConfig (class in nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step) ElasticsearchIndexingStep (class in nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step) EmailManager (class in nanobrain.library.infrastructure.data) (class in nanobrain.library.infrastructure.data.email_manager) embedding_field (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) embedding_model (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) EMBL (nanobrain.core.sequence_manager.SequenceFormat attribute) (nanobrain.core.SequenceFormat attribute), [1] empty_char (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) enable_agent_health_checks (nanobrain.library.infrastructure.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) enable_aliases (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) enable_auth (nanobrain.library.interfaces.web.config.web_interface_config.SecurityConfig attribute) enable_auto_pause (nanobrain.core.resource_monitor.ResourceMonitorConfig attribute) enable_autocomplete (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) enable_caching (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.EEEVAnalysisRequest attribute) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneConfig attribute) enable_circuit_breaker (nanobrain.library.infrastructure.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) enable_colors (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) enable_colors() (nanobrain.library.infrastructure.interfaces.cli.response_formatter.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.cli.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.ResponseFormatter method) enable_conversation_context (nanobrain.library.infrastructure.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) enable_embeddings (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) enable_help (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) enable_history (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) enable_literature_search (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.EEEVAnalysisRequest attribute) enable_logging (nanobrain.AgentConfig attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneConfig attribute) (nanobrain.StepConfig attribute) enable_metrics (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) (nanobrain.library.EnhancedCollaborativeAgent attribute), [1] enable_monitoring (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] enable_notifications (nanobrain.core.resource_monitor.ResourceMonitorConfig attribute) enable_paging (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) enable_plugins (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) enable_progress_bars (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) enable_progress_reporting (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] enable_quit_commands (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) enable_rate_limiting (nanobrain.library.interfaces.web.config.web_interface_config.SecurityConfig attribute) enable_request_logging (nanobrain.library.interfaces.web.config.web_interface_config.LoggingConfig attribute) enable_resource_monitoring (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneConfig attribute) enable_response_caching (nanobrain.library.infrastructure.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) enable_response_logging (nanobrain.library.interfaces.web.config.web_interface_config.LoggingConfig attribute) enable_rich_output (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) enable_rich_text (nanobrain.library.infrastructure.interfaces.cli.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.FormatterConfig attribute) enable_rule() (nanobrain.library.agents.enhanced.delegation_engine.DelegationEngine method) enable_scripting (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) enable_sessions (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) enable_streaming (nanobrain.library.interfaces.web.ChatOptions attribute) (nanobrain.library.interfaces.web.config.web_interface_config.ChatConfig attribute) (nanobrain.library.interfaces.web.models.ChatOptions attribute) (nanobrain.library.interfaces.web.models.request_models.ChatOptions attribute) (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.processing.StreamingHandlerConfig attribute) enable_syntax_highlighting (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) enable_task_caching (nanobrain.core.a2a_support.A2AClientConfig attribute) enable_taxonomy_validation (nanobrain.library.agents.specialized.virus_extraction_agent.VirusExtractionAgent attribute) (nanobrain.library.agents.specialized.VirusExtractionAgent attribute) enable_tool_caching (nanobrain.core.mcp_support.MCPClientConfig attribute) enable_word_wrap (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.FormatterConfig attribute) enable_workflow_metrics (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig attribute) (nanobrain.library.interfaces.web.WebInterfaceConfig attribute) (nanobrain.library.interfaces.WebInterfaceConfig attribute) enabled (nanobrain.core.a2a_support.A2AAgentConfig attribute) (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig attribute) (nanobrain.core.mcp_support.MCPServerConfig attribute) (nanobrain.library.agents.enhanced.delegation_engine.DelegationRule attribute) (nanobrain.library.infrastructure.docker.container_config.DockerComponentConfig attribute) encoding (nanobrain.core.card_schemas.IOSchema attribute) (nanobrain.core.data_unit.DataUnitBase attribute) (nanobrain.core.data_unit.DataUnitConfig attribute) (nanobrain.core.DataUnitBase attribute), [1] (nanobrain.core.DataUnitConfig attribute), [1] (nanobrain.DataUnitConfig attribute) (nanobrain.library.infrastructure.DataUnitBase attribute) end (nanobrain.core.bioinformatics.SequenceCoordinate attribute) (nanobrain.core.SequenceCoordinate attribute), [1] end_time (nanobrain.core.ExecutionContext attribute), [1] (nanobrain.core.logging_system.ExecutionContext attribute) (nanobrain.core.workflow.ProgressStep attribute) (nanobrain.core.workflow.WorkflowProgress attribute) endpoints (nanobrain.library.interfaces.web.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.base_server.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.universal_server.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.servers.UniversalServerConfig attribute) energy_level (nanobrain.core.executor.ExecutorBase attribute) (nanobrain.core.executor.ExecutorBase property) (nanobrain.core.ExecutorBase attribute), [1] (nanobrain.core.ExecutorBase property), [1] enforcement_level (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig attribute) enhance_data_unit_change_trigger() (nanobrain.core.guards.trigger_integration.TriggerGuardIntegration static method) (nanobrain.core.guards.TriggerGuardIntegration static method) enhance_existing_trigger() (in module nanobrain.core.guards) (in module nanobrain.core.guards.trigger_integration) EnhancedAgentConfig (class in nanobrain.core.config.enhanced_config) EnhancedBVBRCDataAcquisitionStep (class in nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step) EnhancedCollaborativeAgent (class in nanobrain.library), [1] (class in nanobrain.library.agents) (class in nanobrain.library.agents.conversational) (class in nanobrain.library.agents.conversational.enhanced_collaborative_agent) EnhancedConfigManager (class in nanobrain.core.config.enhanced_config_manager) EnhancedDataUnitChangeTrigger (class in nanobrain.core.guards) (class in nanobrain.core.guards.trigger_integration) EnhancedToolConfig (class in nanobrain.core.config.enhanced_config) ensure_initialized() (nanobrain.core.external_tool.ExternalTool method) ensure_streaming_enabled() (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest class method) (nanobrain.library.interfaces.web.models.StreamingChatRequest class method) (nanobrain.library.interfaces.web.StreamingChatRequest class method) entity_extraction (nanobrain.library.interfaces.web.analysis.request_analyzer.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.analysis.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.RequestAnalyzerConfig attribute) entry_data (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.CSVMatchCandidate attribute) entry_id (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.WorkflowRegistryEntry attribute) ENUM (nanobrain.core.card_schemas.ParameterType attribute) (nanobrain.core.config.schema_validator.ConstraintType attribute) enum_values (nanobrain.core.card_schemas.ParameterSchema attribute) environment (nanobrain.core.external_tool.ExternalToolConfig attribute) (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneConfig attribute) environment_name (nanobrain.core.external_tool.ExternalToolConfig attribute) (nanobrain.core.external_tool.InstallationStatus attribute) ERROR (nanobrain.core.logging_system.LogLevel attribute) error (nanobrain.core.logging_system.ToolCallLog attribute) ERROR (nanobrain.core.LogLevel attribute), [1] (nanobrain.core.testing.test_constants.TestResult attribute) (nanobrain.core.testing.TestResult attribute) error (nanobrain.core.ToolCallLog attribute), [1] (nanobrain.library.infrastructure.data.chat_session_data.ChatMessage attribute) ERROR (nanobrain.library.infrastructure.data.chat_session_data.MessageType attribute) error (nanobrain.library.infrastructure.data.ChatMessage attribute) ERROR (nanobrain.library.infrastructure.data.MessageType attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.MessageType attribute) error (nanobrain.library.infrastructure.steps.parallel_step.ProcessingResponse attribute) (nanobrain.library.infrastructure.steps.ProcessingResponse attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.api.FrontendErrorResponse attribute) ERROR (nanobrain.library.interfaces.web.api.websocket_router.MessageType attribute) error (nanobrain.library.interfaces.web.ErrorResponse attribute) (nanobrain.library.interfaces.web.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.models.ErrorResponse attribute) (nanobrain.library.interfaces.web.models.response_models.ErrorResponse attribute) ERROR (nanobrain.library.interfaces.web.models.response_models.ResponseStatus attribute) error() (nanobrain.core.async_logging.ProcessSafeLogger method) (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] error_code (nanobrain.library.interfaces.web.ErrorResponse attribute) (nanobrain.library.interfaces.web.models.ErrorResponse attribute) (nanobrain.library.interfaces.web.models.response_models.ErrorResponse attribute) error_count (nanobrain.core.Agent property), [1] (nanobrain.core.agent.Agent property) (nanobrain.core.BaseStep property), [1] (nanobrain.core.link.LinkBase property) (nanobrain.core.LinkBase property), [1] (nanobrain.core.step.BaseStep property) (nanobrain.core.tool.ToolBase property) (nanobrain.core.ToolBase property), [1] (nanobrain.library.infrastructure.data.chat_session_data.InteractionMetrics attribute) error_details (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) (nanobrain.library.interfaces.web.models.universal_models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.UniversalResponse attribute) (nanobrain.library.interfaces.web.WorkflowDiscoveryResult attribute) error_handling (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.Workflow attribute) (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] (nanobrain.library.interfaces.web.processing.response_processor.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.processing.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.ResponseProcessorConfig attribute) error_message (nanobrain.core.agent_logging.AgentInteractionLog attribute) (nanobrain.core.ExecutionContext attribute), [1] (nanobrain.core.logging_system.ExecutionContext attribute) (nanobrain.core.workflow.ProgressStep attribute) (nanobrain.core.workflow.WorkflowProgress attribute) (nanobrain.library.interfaces.web.ChatResponse attribute) (nanobrain.library.interfaces.web.models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.response_models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.StandardizedResponse attribute) (nanobrain.library.interfaces.web.StreamingChatResponse attribute) (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineResult attribute) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.AnalysisProgress attribute) error_message_template (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig attribute) ERROR_NOTIFICATIONS (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingType attribute) (nanobrain.library.interfaces.web.processing.StreamingType attribute) (nanobrain.library.interfaces.web.StreamingType attribute) error_prefix (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) error_value (nanobrain.core.testing.test_result_config.TestResultConfig attribute) (nanobrain.core.testing.TestResultConfig attribute) ErrorHandlingStrategy (class in nanobrain.core), [1] (class in nanobrain.core.workflow) ErrorResponse (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.response_models) estimate_content_size() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) estimated_duration (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.WorkflowExecutionPlan attribute) estimated_processing_time (nanobrain.library.interfaces.web.models.universal_models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.WorkflowMatch attribute) estimated_time (nanobrain.core.workflow.ProgressStep attribute) estimated_total_time (nanobrain.core.workflow.WorkflowProgress attribute) (nanobrain.library.interfaces.web.models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.models.universal_models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.MultiWorkflowRoute attribute)

EVENT_DRIVEN (nanobrain.core.ExecutionStrategy attribute), [1] (nanobrain.core.workflow.ExecutionStrategy attribute) example (nanobrain.core.card_schemas.ParameterSchema attribute) examples (nanobrain.core.a2a_support.A2ASkill attribute) (nanobrain.core.card_schemas.IOSchema attribute) (nanobrain.core.card_schemas.Skill attribute) (nanobrain.core.config.enhanced_config.A2ASkill attribute) (nanobrain.core.prompt_template_manager.PromptTemplate attribute) (nanobrain.core.PromptTemplate attribute), [1] (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) executable_path (nanobrain.core.external_tool.ExternalToolConfig attribute) (nanobrain.core.external_tool.InstallationStatus attribute) execute() (nanobrain.core.Agent method), [1] (nanobrain.core.agent.Agent method) (nanobrain.core.AgentTool method), [1] (nanobrain.core.BaseStep method), [1] (nanobrain.core.executor.ExecutorBase method) (nanobrain.core.executor.LocalExecutor method) (nanobrain.core.executor.ParslExecutor method) (nanobrain.core.executor.ProcessExecutor method) (nanobrain.core.executor.ThreadExecutor method) (nanobrain.core.ExecutorBase method), [1] (nanobrain.core.FunctionTool method), [1] (nanobrain.core.guards.examples.protected_step_example.ProtectedStepExample method) (nanobrain.core.LangChainTool method), [1] (nanobrain.core.LocalExecutor method), [1] (nanobrain.core.mcp_support.MCPTool method) (nanobrain.core.ParslExecutor method), [1] (nanobrain.core.ProcessExecutor method), [1] (nanobrain.core.step.BaseStep method) (nanobrain.core.StepTool method), [1] (nanobrain.core.ThreadExecutor method), [1] (nanobrain.core.tool.AgentTool method) (nanobrain.core.tool.FunctionTool method) (nanobrain.core.tool.LangChainTool method) (nanobrain.core.tool.StepTool method) (nanobrain.core.tool.ToolBase method) (nanobrain.core.ToolBase method), [1] (nanobrain.library.infrastructure.DatabaseInterface method) (nanobrain.library.infrastructure.interfaces.database.DatabaseInterface method) (nanobrain.library.infrastructure.interfaces.DatabaseInterface method) (nanobrain.library.workflows.viral_protein_analysis.steps.alignment_step.AlignmentStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.AlignmentStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step.BVBRCDataAcquisitionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.BVBRCDataAcquisitionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.clustering_step.ClusteringStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.ClusteringStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step.BVBRCDataAcquisitionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_aggregation_step.DataAggregationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.DataAggregationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.pssm_analysis_step.PSSMAnalysisStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.PSSMAnalysisStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.result_collection_step.ResultCollectionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.ResultCollectionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.sequence_curation_step.SequenceCurationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.SequenceCurationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.viral_pssm_generation_step.ViralPSSMGenerationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.ViralPSSMGenerationStep method) (nanobrain.LocalExecutor method) (nanobrain.ParslExecutor method) execute_command() (nanobrain.core.external_tool.ExternalTool method) (nanobrain.library.infrastructure.BaseCLI method) (nanobrain.library.infrastructure.interfaces.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.base_cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.BaseCLI method) execute_fallback_workflows() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) execute_pipeline() (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.BVBRCCommandPipeline method) execute_route() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) execute_tool() (nanobrain.core.bioinformatics.ExternalToolManager method) (nanobrain.core.ExternalToolManager method), [1] (nanobrain.core.tool.ToolRegistry method) (nanobrain.core.ToolRegistry method), [1] execute_with_progressive_scaling() (nanobrain.core.progressive_scaling.ProgressiveScalingMixin method) execute_with_tool() (nanobrain.library.agents.specialized.base.BaseAgent method) execute_workflow() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) execution_config (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.WorkflowRouterConfig attribute) execution_context (nanobrain.core.agent_logging.AgentInteractionLog attribute) (nanobrain.core.async_logging.LogMessage attribute) execution_context() (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] execution_count (nanobrain.core.Agent property), [1] (nanobrain.core.agent.Agent property) (nanobrain.core.BaseStep property), [1] (nanobrain.core.step.BaseStep property) execution_progress (nanobrain.library.interfaces.web.models.response_models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.WorkflowStatusResponse attribute) execution_strategy (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.Workflow attribute) (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] (nanobrain.library.interfaces.web.models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.models.universal_models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.WorkflowExecutionPlan attribute) execution_time (nanobrain.core.external_tool.ToolResult attribute) (nanobrain.library.infrastructure.data.AnnotationJobData property) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData property) (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.CommandResult attribute) (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineResult attribute) ExecutionContext (class in nanobrain.core), [1] (class in nanobrain.core.logging_system) ExecutionStrategy (class in nanobrain.core), [1] (class in nanobrain.core.workflow) executor (nanobrain.core.Agent attribute), [1] (nanobrain.core.agent.Agent attribute) (nanobrain.core.BaseStep attribute), [1] (nanobrain.core.step.BaseStep attribute) (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.Workflow attribute) executor_config (nanobrain.AgentConfig attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.StepConfig attribute) EXECUTOR_RUN (nanobrain.core.logging_system.OperationType attribute) (nanobrain.core.OperationType attribute), [1] executor_type (nanobrain.core.executor.ExecutorBase attribute) (nanobrain.core.executor.ExecutorConfig attribute) (nanobrain.core.ExecutorBase attribute), [1] (nanobrain.core.ExecutorConfig attribute), [1] (nanobrain.ExecutorConfig attribute) ExecutorBase (class in nanobrain.core), [1] (class in nanobrain.core.executor) ExecutorConfig (class in nanobrain) (class in nanobrain.core), [1] (class in nanobrain.core.executor) executors (nanobrain.core.config.yaml_config.YAMLWorkflowConfig attribute) ExecutorType (class in nanobrain.core.executor) expected_exception (nanobrain.library.infrastructure.CircuitBreaker attribute) (nanobrain.library.infrastructure.load_balancing.circuit_breaker.CircuitBreaker attribute) (nanobrain.library.infrastructure.load_balancing.CircuitBreaker attribute) expected_output (nanobrain.core.card_schemas.UsageExample attribute) (nanobrain.core.config.enhanced_config.UsageExample attribute) expected_proteins (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneConfig attribute) expertise_level (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.config.enhanced_config.AgentCardSection attribute) expires_at (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData attribute) (nanobrain.library.infrastructure.data.ChatSessionData attribute) EXPLANATION_REQUEST (nanobrain.library.interfaces.web.IntentType attribute) (nanobrain.library.interfaces.web.models.IntentType attribute) (nanobrain.library.interfaces.web.models.universal_models.IntentType attribute) export_a2a_cards() (in module nanobrain.core.config.enhanced_config_manager) (nanobrain.core.config.enhanced_config_manager.EnhancedConfigManager method), [1] export_agent_card() (nanobrain.core.config.enhanced_config.EnhancedAgentConfig method) export_cache (nanobrain.core.config.enhanced_config_manager.EnhancedConfigManager attribute) export_conversations() (nanobrain.library.ConversationHistoryUnit method), [1] (nanobrain.library.infrastructure.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.conversation_history.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.ConversationHistoryUnit method) export_data() (nanobrain.library.infrastructure.data.export_manager.ExportManager method) (nanobrain.library.infrastructure.data.ExportManager method) (nanobrain.library.infrastructure.ExportManager method) export_metrics() (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor method) (nanobrain.library.infrastructure.PerformanceMonitor method) export_multiple_data_units() (nanobrain.library.infrastructure.data.export_manager.ExportManager method) (nanobrain.library.infrastructure.data.ExportManager method) (nanobrain.library.infrastructure.ExportManager method) export_rules() (nanobrain.library.agents.enhanced.delegation_engine.DelegationEngine method) export_sessions() (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.SessionManager method) ExportManager (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.data) (class in nanobrain.library.infrastructure.data.export_manager) extend_session() (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.SessionManager method) EXTERNAL (nanobrain.core.tool.ToolType attribute) (nanobrain.core.ToolType attribute), [1] EXTERNAL_NAME (nanobrain.library.infrastructure.docker.container_config.ServiceType attribute) external_tools_timeout (nanobrain.core.bioinformatics.BioinformaticsConfig attribute) (nanobrain.core.BioinformaticsConfig attribute), [1] ExternalTool (class in nanobrain.core.external_tool) ExternalToolConfig (class in nanobrain.core.external_tool) ExternalToolError ExternalToolManager (class in nanobrain.core), [1] (class in nanobrain.core.bioinformatics) extract_analysis_types() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) extract_component_config() (nanobrain.core.BaseStep class method), [1] (nanobrain.core.component_base.FromConfigBase class method) (nanobrain.core.ConditionalLink class method), [1] (nanobrain.core.data_unit.DataUnitBase class method) (nanobrain.core.DataUnitBase class method), [1] (nanobrain.core.DirectLink class method), [1] (nanobrain.core.executor.ExecutorBase class method) (nanobrain.core.ExecutorBase class method), [1] (nanobrain.core.external_tool.ExternalTool class method) (nanobrain.core.FromConfigBase class method), [1] (nanobrain.core.link.ConditionalLink class method) (nanobrain.core.link.DirectLink class method) (nanobrain.core.link.LinkBase class method) (nanobrain.core.LinkBase class method), [1] (nanobrain.core.Step class method), [1] (nanobrain.core.step.BaseStep class method) (nanobrain.core.step.Step class method) (nanobrain.core.step.TransformStep class method) (nanobrain.core.tool.ToolBase class method) (nanobrain.core.ToolBase class method), [1] (nanobrain.core.TransformStep class method), [1] (nanobrain.core.trigger.DataUnitChangeTrigger class method) (nanobrain.core.trigger.TriggerBase class method) (nanobrain.core.TriggerBase class method), [1] (nanobrain.core.Workflow class method), [1] (nanobrain.core.workflow.Workflow class method) (nanobrain.DirectLink class method) (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent class method) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent class method) (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent class method) (nanobrain.library.agents.EnhancedCollaborativeAgent class method) (nanobrain.library.agents.SimpleSpecializedAgent class method) (nanobrain.library.agents.specialized.base.SimpleSpecializedAgent class method) (nanobrain.library.agents.specialized.SimpleSpecializedAgent class method) (nanobrain.library.ChatWorkflow class method), [1] (nanobrain.library.EnhancedCollaborativeAgent class method), [1] (nanobrain.library.infrastructure.DataUnitBase class method) (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase class method) (nanobrain.library.infrastructure.docker.container_config.DockerComponentBase class method) (nanobrain.library.interfaces.web.web_interface.WebInterface class method) (nanobrain.library.interfaces.web.WebInterface class method) (nanobrain.library.interfaces.WebInterface class method) (nanobrain.library.workflows.ChatWorkflow class method) (nanobrain.library.workflows.viral_protein_analysis.steps.clustering_step.ClusteringStep class method) (nanobrain.library.workflows.viral_protein_analysis.steps.ClusteringStep class method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_aggregation_step.DataAggregationStep class method) (nanobrain.library.workflows.viral_protein_analysis.steps.DataAggregationStep class method) (nanobrain.library.workflows.viral_protein_analysis.steps.result_collection_step.ResultCollectionStep class method) (nanobrain.library.workflows.viral_protein_analysis.steps.ResultCollectionStep class method) (nanobrain.library.workflows.viral_protein_analysis.steps.viral_pssm_generation_step.ViralPSSMGenerationStep class method) (nanobrain.library.workflows.viral_protein_analysis.steps.ViralPSSMGenerationStep class method) (nanobrain.Step class method) extract_domain_keywords() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) extract_entities_async() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) extract_intent_async() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) extract_protein_sequences() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) extract_response_content() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) extract_subsequence() (nanobrain.core.sequence_manager.SequenceManager method) (nanobrain.core.SequenceManager method), [1] extract_template_params() (nanobrain.core.prompt_template_manager.PromptTemplateManager method) (nanobrain.core.PromptTemplateManager method), [1] extract_virus_names() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) extract_workflow_capabilities() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) extracted_entities (nanobrain.library.interfaces.web.models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.models.universal_models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.RequestAnalysis attribute) extracted_parameters (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.QueryClassificationData attribute) (nanobrain.library.infrastructure.data.QueryClassificationData attribute) extraction_agent (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.StepConfig attribute) extraction_confidence_threshold (nanobrain.library.agents.specialized.virus_extraction_agent.VirusExtractionAgent attribute) (nanobrain.library.agents.specialized.VirusExtractionAgent attribute) extraction_prompt_template (nanobrain.library.agents.specialized.virus_extraction_agent.VirusExtractionAgent attribute) (nanobrain.library.agents.specialized.VirusExtractionAgent attribute)

F

factory_config (nanobrain.library.interfaces.web.ServerFactoryConfig attribute) (nanobrain.library.interfaces.web.servers.server_factory.ServerFactoryConfig attribute) (nanobrain.library.interfaces.web.servers.ServerFactoryConfig attribute) FAIL (nanobrain.core.testing.test_constants.TestResult attribute) (nanobrain.core.testing.TestResult attribute) fail_on_agent_error (nanobrain.core.a2a_support.A2AClientConfig attribute) fail_on_server_error (nanobrain.core.mcp_support.MCPClientConfig attribute) fail_value (nanobrain.core.testing.test_result_config.TestResultConfig attribute) (nanobrain.core.testing.TestResultConfig attribute) fail_with_error() (nanobrain.library.infrastructure.data.AnnotationJobData method) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData method) FAILED (nanobrain.core.a2a_support.TaskStatus attribute) failed_annotations (nanobrain.library.infrastructure.data.chat_session_data.InteractionMetrics attribute) FAILURE (nanobrain.core.testing.test_constants.TestResult attribute) (nanobrain.core.testing.TestResult attribute) failure_count (nanobrain.library.infrastructure.CircuitBreaker attribute) (nanobrain.library.infrastructure.load_balancing.circuit_breaker.CircuitBreaker attribute) (nanobrain.library.infrastructure.load_balancing.CircuitBreaker attribute) failure_threshold (nanobrain.library.infrastructure.CircuitBreaker attribute) (nanobrain.library.infrastructure.docker.container_config.HealthCheckConfig attribute) (nanobrain.library.infrastructure.load_balancing.circuit_breaker.CircuitBreaker attribute) (nanobrain.library.infrastructure.load_balancing.CircuitBreaker attribute) failure_value (nanobrain.core.testing.test_result_config.TestResultConfig attribute) (nanobrain.core.testing.TestResultConfig attribute) FALLBACK_CHAIN (nanobrain.library.interfaces.web.models.RoutingStrategy attribute) (nanobrain.library.interfaces.web.models.universal_models.RoutingStrategy attribute) (nanobrain.library.interfaces.web.RoutingStrategy attribute) fallback_config (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.WorkflowRouterConfig attribute) fallback_domain_classification() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) fallback_intent_classification() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) fallback_plans (nanobrain.library.interfaces.web.models.workflow_models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.WorkflowExecutionPlan attribute) fallback_strategy (nanobrain.library.interfaces.web.routing.routing_strategies.RoutingStrategyConfig attribute) (nanobrain.library.interfaces.web.routing.RoutingStrategyConfig attribute) fallback_workflows (nanobrain.library.interfaces.web.models.universal_models.WorkflowRoute attribute) (nanobrain.library.interfaces.web.models.WorkflowRoute attribute) (nanobrain.library.interfaces.web.WorkflowRoute attribute) FASTA (nanobrain.core.sequence_manager.SequenceFormat attribute) (nanobrain.core.SequenceFormat attribute), [1] FastaParser (class in nanobrain.core), [1] (class in nanobrain.core.sequence_manager) fastapi_config (nanobrain.library.interfaces.web.servers.universal_server.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.servers.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.UniversalServerConfig attribute) FASTEST_RESPONSE (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.load_balancing.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.steps.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.steps.parallel_step.LoadBalancingStrategy attribute) FASTQ (nanobrain.core.sequence_manager.SequenceFormat attribute) (nanobrain.core.SequenceFormat attribute), [1] feature_count (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineResult attribute) features_id_md5 (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineFiles attribute) field_type (nanobrain.core.config.schema_validator.FieldSchema attribute) FieldConstraint (class in nanobrain.core.config.schema_validator) fields (nanobrain.core.config.schema_validator.ConfigSchema attribute) (nanobrain.core.config.schema_validator.ParameterSchema attribute) (nanobrain.core.config.schema_validator.ValidatorFunction attribute) FieldSchema (class in nanobrain.core.config.schema_validator) FieldType (class in nanobrain.core.config.schema_validator) file (nanobrain.core.a2a_support.A2APart attribute) FILE (nanobrain.core.a2a_support.PartType attribute) (nanobrain.core.card_schemas.InputMode attribute) (nanobrain.core.card_schemas.OutputMode attribute) (nanobrain.core.link.LinkType attribute) (nanobrain.core.LinkType attribute), [1] FILE_DOWNLOAD (nanobrain.library.interfaces.web.models.OutputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.OutputType attribute) (nanobrain.library.interfaces.web.OutputType attribute) file_exists() (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin method) file_keywords (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin attribute) file_operation_patterns (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin attribute) FILE_PATH (nanobrain.core.card_schemas.ParameterType attribute) file_path (nanobrain.core.data_unit.DataUnitBase attribute) (nanobrain.core.data_unit.DataUnitConfig attribute) (nanobrain.core.DataUnitBase attribute), [1] (nanobrain.core.DataUnitConfig attribute), [1] (nanobrain.core.link.LinkConfig attribute) (nanobrain.core.LinkConfig attribute), [1] (nanobrain.DataUnitConfig attribute) (nanobrain.library.infrastructure.DataUnitBase attribute) (nanobrain.LinkConfig attribute) file_paths (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusCacheEntry attribute) FILE_UPLOAD (nanobrain.library.interfaces.web.InputType attribute) (nanobrain.library.interfaces.web.models.InputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.InputType attribute) FileLink (class in nanobrain.core), [1] (class in nanobrain.core.link) files (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineResult attribute) FileSystemInterface (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.external) FileWriterAgent (class in nanobrain.library.agents) (class in nanobrain.library.agents.specialized) (class in nanobrain.library.agents.specialized.file_writer) FileWriterAgentMixin (class in nanobrain.library.agents.specialized.file_writer) fill_char (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) final_validation (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.CSVMatchCandidate attribute) finalize_stream() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) find_orfs() (nanobrain.core.sequence_manager.SequenceManager method) (nanobrain.core.SequenceManager method), [1] find_workflow_classes_in_module() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) fire() (nanobrain.core.ManualTrigger method), [1] (nanobrain.core.trigger.ManualTrigger method) flags (nanobrain.library.infrastructure.interfaces.cli.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.CLIContext attribute) FLOAT (nanobrain.core.card_schemas.ParameterType attribute) (nanobrain.core.config.schema_validator.FieldType attribute) flush_stream_buffer() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) FORM_BASED (nanobrain.library.interfaces.web.InteractionPattern attribute) (nanobrain.library.interfaces.web.models.InteractionPattern attribute) (nanobrain.library.interfaces.web.models.workflow_models.InteractionPattern attribute) format (nanobrain.core.card_schemas.IOSchema attribute) format_command_result() (nanobrain.library.infrastructure.interfaces.cli.response_formatter.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.cli.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.ResponseFormatter method) format_converter (nanobrain.library.interfaces.web.processing.response_processor.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.ResponseProcessorConfig attribute) format_error() (nanobrain.library.infrastructure.interfaces.cli.response_formatter.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.cli.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.ResponseFormatter method) format_for_web() (nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow.WebResultFormatter method) (nanobrain.library.workflows.viral_protein_analysis.web.WebResultFormatter method) format_info() (nanobrain.library.infrastructure.interfaces.cli.response_formatter.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.cli.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.ResponseFormatter method) format_output() (nanobrain.library.infrastructure.interfaces.cli.response_formatter.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.cli.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.ResponseFormatter method) format_response() (nanobrain.library.workflows.conversational.viral_expert_workflow.ConversationalResponseFormatter method) format_schema (nanobrain.core.config.enhanced_config.InputOutputFormat attribute) format_settings (nanobrain.library.interfaces.web.processing.format_converter.FormatConverterConfig attribute) (nanobrain.library.interfaces.web.processing.FormatConverterConfig attribute) format_simple_output() (in module nanobrain.library.infrastructure.interfaces.cli.response_formatter) format_success() (nanobrain.library.infrastructure.interfaces.cli.response_formatter.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.cli.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.ResponseFormatter method) format_warning() (nanobrain.library.infrastructure.interfaces.cli.response_formatter.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.cli.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.ResponseFormatter method)

format_with_references() (nanobrain.library.infrastructure.data.chat_session_data.ConversationalResponseData method) (nanobrain.library.infrastructure.data.ConversationalResponseData method) FormatConverter (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.processing) (class in nanobrain.library.interfaces.web.processing.format_converter) FormatConverterConfig (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.processing) (class in nanobrain.library.interfaces.web.processing.format_converter) FormatterConfig (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.cli) (class in nanobrain.library.infrastructure.interfaces.cli.response_formatter) found (nanobrain.core.external_tool.InstallationStatus attribute) framework_integration (nanobrain.library.interfaces.web.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.base_server.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.universal_server.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.servers.UniversalServerConfig attribute) framework_metadata (nanobrain.core.config.enhanced_config.EnhancedAgentConfig attribute) (nanobrain.core.config.enhanced_config.EnhancedToolConfig attribute) free_bytes (nanobrain.core.resource_monitor.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.DiskSpaceInfo attribute) free_gb (nanobrain.core.resource_monitor.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.DiskSpaceInfo attribute) from_config() (nanobrain.core.AgentTool class method), [1] (nanobrain.core.AllDataReceivedTrigger class method), [1] (nanobrain.core.component_base.FromConfigBase class method) (nanobrain.core.ConditionalLink class method), [1] (nanobrain.core.config.config_base.ConfigBase class method) (nanobrain.core.config.ConfigBase class method) (nanobrain.core.config.yaml_config.YAMLConfig method) (nanobrain.core.config.YAMLConfig method) (nanobrain.core.data_unit.DataUnit class method) (nanobrain.core.data_unit.DataUnitFile class method) (nanobrain.core.data_unit.DataUnitMemory class method) (nanobrain.core.data_unit.DataUnitStream class method) (nanobrain.core.data_unit.DataUnitString class method) (nanobrain.core.DataUnitFile class method), [1] (nanobrain.core.DataUnitMemory class method), [1] (nanobrain.core.DataUnitStream class method), [1] (nanobrain.core.DataUnitString class method), [1] (nanobrain.core.DataUpdatedTrigger class method), [1] (nanobrain.core.DirectLink class method), [1] (nanobrain.core.executor.LocalExecutor class method) (nanobrain.core.executor.ParslExecutor class method) (nanobrain.core.executor.ProcessExecutor class method) (nanobrain.core.executor.ThreadExecutor class method) (nanobrain.core.FromConfigBase class method), [1] (nanobrain.core.FunctionTool class method), [1] (nanobrain.core.LangChainTool class method), [1] (nanobrain.core.link.ConditionalLink class method) (nanobrain.core.link.DirectLink class method) (nanobrain.core.LocalExecutor class method), [1] (nanobrain.core.ManualTrigger class method), [1] (nanobrain.core.mcp_support.MCPTool class method) (nanobrain.core.ParslExecutor class method), [1] (nanobrain.core.ProcessExecutor class method), [1] (nanobrain.core.StepTool class method), [1] (nanobrain.core.ThreadExecutor class method), [1] (nanobrain.core.TimerTrigger class method), [1] (nanobrain.core.tool.AgentTool class method) (nanobrain.core.tool.FunctionTool class method) (nanobrain.core.tool.LangChainTool class method) (nanobrain.core.tool.StepTool class method) (nanobrain.core.trigger.AllDataReceivedTrigger class method) (nanobrain.core.trigger.DataUnitChangeTrigger class method) (nanobrain.core.trigger.DataUpdatedTrigger class method) (nanobrain.core.trigger.ManualTrigger class method) (nanobrain.core.trigger.TimerTrigger class method) (nanobrain.core.Workflow class method), [1] (nanobrain.core.workflow.Workflow class method) (nanobrain.DataUnitMemory class method) (nanobrain.DataUpdatedTrigger class method) (nanobrain.DirectLink class method) (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent class method) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent class method) (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent class method) (nanobrain.library.agents.EnhancedCollaborativeAgent class method) (nanobrain.library.agents.specialized.base.BaseAgent class method) (nanobrain.library.DataUnitMemory class method), [1] (nanobrain.library.EnhancedCollaborativeAgent class method), [1] (nanobrain.library.infrastructure.DataUnitFile class method) (nanobrain.library.infrastructure.DataUnitMemory class method) (nanobrain.library.infrastructure.DataUnitStream class method) (nanobrain.library.infrastructure.DataUnitString class method) (nanobrain.library.infrastructure.docker.container_config.ContainerConfig class method) (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase class method) (nanobrain.library.infrastructure.docker.container_config.DockerComponentBase class method) (nanobrain.library.interfaces.web.BaseUniversalServer class method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer class method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer class method) (nanobrain.library.interfaces.web.web_interface.WebInterface class method) (nanobrain.library.interfaces.web.WebInterface class method) (nanobrain.library.interfaces.WebInterface class method) (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingStep class method) (nanobrain.LocalExecutor class method) (nanobrain.ParslExecutor class method) from_config_file() (nanobrain.library.interfaces.web.web_interface.WebInterface class method) (nanobrain.library.interfaces.web.WebInterface class method) (nanobrain.library.interfaces.WebInterface class method) from_dict() (nanobrain.core.a2a_support.A2AAgentCard class method) (nanobrain.core.a2a_support.A2AAgentConfig class method) (nanobrain.core.a2a_support.A2AClientConfig class method) (nanobrain.core.card_schemas.AgentCard class method) (nanobrain.core.card_schemas.ToolCard class method) (nanobrain.core.mcp_support.MCPClientConfig class method) (nanobrain.core.mcp_support.MCPServerConfig class method) (nanobrain.core.workflow.ProgressStep class method) (nanobrain.core.workflow.WorkflowProgress class method) (nanobrain.library.interfaces.web.api.websocket_router.WebSocketMessage class method) (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig class method) (nanobrain.library.interfaces.web.WebInterfaceConfig class method) (nanobrain.library.interfaces.WebInterfaceConfig class method) from_yaml() (nanobrain.AgentConfig class method) (nanobrain.core.agent.AgentConfig class method) (nanobrain.core.AgentConfig class method), [1] (nanobrain.core.config.yaml_config.YAMLConfig class method) (nanobrain.core.config.YAMLConfig class method) (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig class method) (nanobrain.library.interfaces.web.WebInterfaceConfig class method) (nanobrain.library.interfaces.WebInterfaceConfig class method) from_yaml_config() (nanobrain.core.a2a_support.A2AClient class method) (nanobrain.core.mcp_support.MCPClient class method) FromConfigBase (class in nanobrain.core), [1] (class in nanobrain.core.component_base) frontend_chat() (in module nanobrain.library.interfaces.web.api.frontend_router) frontend_health_check() (in module nanobrain.library.interfaces.web.api.frontend_router) frontend_hints (nanobrain.library.interfaces.web.models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.StandardizedResponse attribute) frontend_optimization (nanobrain.library.interfaces.web.processing.response_processor.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.ResponseProcessorConfig attribute) FrontendChatRequest (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.api) (class in nanobrain.library.interfaces.web.api.frontend_router) FrontendChatResponse (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.api) (class in nanobrain.library.interfaces.web.api.frontend_router) FrontendErrorResponse (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.api) (class in nanobrain.library.interfaces.web.api.frontend_router) FrontendHealthResponse (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.api) (class in nanobrain.library.interfaces.web.api.frontend_router) full_image (nanobrain.library.infrastructure.docker.container_config.ContainerConfig property) FUNCTION (nanobrain.core.tool.ToolType attribute) (nanobrain.core.ToolType attribute), [1] function_tool() (in module nanobrain.core.tool) FunctionTool (class in nanobrain.core), [1] (class in nanobrain.core.tool)

G

gc_content (nanobrain.core.sequence_manager.SequenceStats attribute) (nanobrain.core.SequenceStats attribute), [1] GENBANK (nanobrain.core.sequence_manager.SequenceFormat attribute) (nanobrain.core.SequenceFormat attribute), [1] GENERAL_CONVERSATION (nanobrain.library.interfaces.web.IntentType attribute) (nanobrain.library.interfaces.web.models.IntentType attribute) (nanobrain.library.interfaces.web.models.universal_models.IntentType attribute) GENERAL_SCIENCE (nanobrain.library.interfaces.web.DomainType attribute) (nanobrain.library.interfaces.web.models.DomainType attribute) (nanobrain.library.interfaces.web.models.universal_models.DomainType attribute) generate_a2a_card() (nanobrain.core.config.enhanced_config.EnhancedAgentConfig method), [1] generate_all_schemas() (in module nanobrain.core.config.schema_generator) generate_config_templates() (nanobrain.core.config.enhanced_config_manager.EnhancedConfigManager method) generate_context_key() (nanobrain.library.interfaces.web.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.AdaptiveStrategy method) generate_example_data() (nanobrain.core.config.schema_generator.SchemaGenerator method) generate_frontend_hints() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) generate_nanobrain_step() (nanobrain.library.agents.specialized.code_writer.CodeWriterAgentMixin method) generate_python_class() (nanobrain.library.agents.specialized.code_writer.CodeWriterAgentMixin method) generate_python_function() (nanobrain.library.agents.specialized.code_writer.CodeWriterAgentMixin method) generate_schema() (in module nanobrain.core.config.schema_generator) (nanobrain.core.config.schema_generator.SchemaGenerator method), [1] generate_schema_template() (nanobrain.core.config.schema_validator.SchemaValidator method) generate_standardized_message() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) generate_templates() (in module nanobrain.core.config.enhanced_config_manager) generate_tool_card() (nanobrain.core.config.enhanced_config.EnhancedToolConfig method) generate_ui_schema() (nanobrain.core.config.schema_generator.SchemaGenerator method) generate_workflow_id() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) generate_workflow_schema() (nanobrain.core.config.schema_generator.SchemaGenerator method), [1] genome_count (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineResult attribute) (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.TaxonInfo attribute) genome_size_kb (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneConfig attribute) GenomeData (class in nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step) (class in nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step) genomes_tsv (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineFiles attribute) GENOMICS (nanobrain.library.interfaces.web.DomainType attribute) (nanobrain.library.interfaces.web.models.DomainType attribute) (nanobrain.library.interfaces.web.models.universal_models.DomainType attribute) get() (nanobrain.core.bioinformatics.BioinformaticsDataUnit method) (nanobrain.core.BioinformaticsDataUnit method), [1] (nanobrain.core.config.component_factory.ComponentRegistry class method) (nanobrain.core.data_unit.DataUnit method) (nanobrain.core.data_unit.DataUnitBase method) (nanobrain.core.data_unit.DataUnitFile method) (nanobrain.core.data_unit.DataUnitMemory method) (nanobrain.core.data_unit.DataUnitStream method) (nanobrain.core.data_unit.DataUnitString method) (nanobrain.core.DataUnitBase method), [1] (nanobrain.core.DataUnitFile method), [1] (nanobrain.core.DataUnitMemory method), [1] (nanobrain.core.DataUnitStream method), [1] (nanobrain.core.DataUnitString method), [1] (nanobrain.core.tool.ToolRegistry method) (nanobrain.core.ToolRegistry method), [1] (nanobrain.DataUnitMemory method) (nanobrain.library.ConversationHistoryUnit method), [1] (nanobrain.library.DataUnitMemory method), [1] (nanobrain.library.infrastructure.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.conversation_history.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.export_manager.ExportManager method) (nanobrain.library.infrastructure.data.ExportManager method) (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.DataUnitBase method) (nanobrain.library.infrastructure.DataUnitFile method) (nanobrain.library.infrastructure.DataUnitMemory method) (nanobrain.library.infrastructure.DataUnitStream method) (nanobrain.library.infrastructure.DataUnitString method) (nanobrain.library.infrastructure.ExportManager method) (nanobrain.library.infrastructure.interfaces.APIInterface method) (nanobrain.library.infrastructure.interfaces.external.APIInterface method) (nanobrain.library.infrastructure.load_balancing.request_queue.RequestQueue method) (nanobrain.library.infrastructure.load_balancing.RequestQueue method) (nanobrain.library.infrastructure.RequestQueue method) (nanobrain.library.infrastructure.SessionManager method) get_a2a_agent_capabilities() (nanobrain.core.a2a_support.A2ASupportMixin method) get_a2a_agents() (nanobrain.core.a2a_support.A2ASupportMixin method) get_a2a_status() (nanobrain.core.a2a_support.A2ASupportMixin method) get_active_connections() (nanobrain.library.interfaces.web.api.websocket_router.ConnectionManager method) get_active_job_count() (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData method) (nanobrain.library.infrastructure.data.ChatSessionData method) get_active_session_count() (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.SessionManager method) get_adaptive_threshold_adjustment() (nanobrain.library.interfaces.web.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.AdaptiveStrategy method) get_agent_card() (nanobrain.core.card_schemas.CardManager method) get_agent_config() (nanobrain.core.config.yaml_config.YAMLWorkflowConfig method) get_agent_guard() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_trigger_guard) get_agent_stats() (nanobrain.library.infrastructure.ParallelAgentStep method) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentStep method) (nanobrain.library.infrastructure.steps.ParallelAgentStep method) (nanobrain.library.ParallelAgentStep method), [1] get_alerts() (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor method) (nanobrain.library.infrastructure.PerformanceMonitor method) get_all_agents() (nanobrain.core.a2a_support.A2AClient method) get_all_capabilities() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) get_all_scale_levels() (nanobrain.core.progressive_scaling.ProgressiveScalingMixin method) get_all_tools() (nanobrain.core.mcp_support.MCPClient method) get_all_trigger_states() (in module nanobrain.core.guards) (in module nanobrain.core.guards.contextvar_core) get_api_key() (in module nanobrain.core.config.config_manager) (nanobrain.core.config.config_manager.ConfigManager method) get_available_collaborators() (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent method) get_available_providers() (nanobrain.core.config.config_manager.ConfigManager method) get_available_server_types() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory method) (nanobrain.library.interfaces.web.UniversalServerFactory method) get_available_taxa() (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.VirusNameResolver method) get_cache_identifier() (nanobrain.library.workflows.viral_protein_analysis.base_cache_manager.BaseCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.BaseCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusSpecificCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.VirusSpecificCacheManager method) get_cache_key() (nanobrain.library.infrastructure.data.email_manager.EmailManager method) (nanobrain.library.infrastructure.data.EmailManager method) get_cache_statistics() (nanobrain.library.infrastructure.data.cache_manager.CacheManager method) (nanobrain.library.infrastructure.data.CacheManager method) get_cache_stats() (nanobrain.library.workflows.viral_protein_analysis.base_cache_manager.BaseCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.BaseCacheManager method) get_cached_analysis() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) get_cached_bvbrc_result() (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusSpecificCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.VirusSpecificCacheManager method) get_cached_execution() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) get_cached_file() (nanobrain.library.workflows.viral_protein_analysis.base_cache_manager.BaseCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.BaseCacheManager method) get_cached_response() (nanobrain.library.infrastructure.data.cache_manager.CacheManager method) (nanobrain.library.infrastructure.data.CacheManager method) get_cached_result() (nanobrain.library.workflows.viral_protein_analysis.base_cache_manager.BaseCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.BaseCacheManager method) get_cached_route() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) get_cached_sequence() (nanobrain.core.sequence_manager.SequenceManager method) (nanobrain.core.SequenceManager method), [1] get_cached_virus_data() (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusSpecificCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.VirusSpecificCacheManager method) get_card_manager() (in module nanobrain.core.card_schemas) get_chat_stats() (nanobrain.library.infrastructure.ParallelConversationalAgentStep method) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentStep method) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentStep method) (nanobrain.library.ParallelConversationalAgentStep method), [1] get_chat_workflow() (in module nanobrain.library.interfaces.web.api.chat_router) (in module nanobrain.library.interfaces.web.api.frontend_router) (in module nanobrain.library.interfaces.web.api.websocket_router) get_class_guard_scope() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_enforcer_meta) get_class_protected_methods() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_enforcer_meta) get_collaboration_history() (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent method) get_command_help() (nanobrain.library.infrastructure.interfaces.cli.command_processor.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.cli.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.CommandProcessor method) get_command_suggestions() (nanobrain.library.infrastructure.interfaces.cli.command_processor.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.cli.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.CommandProcessor method) get_compatible_workflows() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRouter method) get_component_class() (in module nanobrain.core.config.component_factory) get_config() (nanobrain.core.config.config_manager.ConfigManager method) get_config_dict() (nanobrain.core.config.config_manager.ConfigManager method) get_config_manager() (in module nanobrain) (in module nanobrain.core.config.config_manager) get_config_with_env_overrides() (in module nanobrain.library.interfaces.web.config) get_connection() (nanobrain.library.infrastructure.interfaces.database.ConnectionPool method) get_connection_count() (nanobrain.library.interfaces.web.api.websocket_router.ConnectionManager method) get_connection_manager() (in module nanobrain.library.interfaces.web.api) (in module nanobrain.library.interfaces.web.api.websocket_router) get_console_log_config() (nanobrain.core.config.config_manager.ConfigManager method) get_container_logs() (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase method) get_container_status() (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase method) get_context_adjustment() (nanobrain.library.interfaces.web.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.AdaptiveStrategy method) get_context_var_name() (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig method) (nanobrain.core.guards.NanobrainTriggerGuardConfig method) get_conversation_details() (in module nanobrain.library.interfaces.web.api.frontend_router) get_conversation_history() (in module nanobrain.library.interfaces.web.api.chat_router) (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] (nanobrain.library.ConversationHistoryUnit method), [1] (nanobrain.library.infrastructure.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData method) (nanobrain.library.infrastructure.data.ChatSessionData method) (nanobrain.library.infrastructure.data.conversation_history.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.ConversationHistoryUnit method) get_conversation_stats() (nanobrain.library.ChatWorkflow method), [1] (nanobrain.library.workflows.ChatWorkflow method) get_conversations() (in module nanobrain.library.interfaces.web.api.frontend_router) get_converter() (nanobrain.library.interfaces.web.FormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverter method) (nanobrain.library.interfaces.web.processing.FormatConverter method) get_current_metrics() (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor method) (nanobrain.library.infrastructure.PerformanceMonitor method) get_current_step() (nanobrain.core.workflow.WorkflowProgress method) get_default_model() (in module nanobrain.core.config.config_manager) (nanobrain.core.config.config_manager.ConfigManager method) get_email_for_service() (nanobrain.library.infrastructure.data.email_manager.EmailManager method) (nanobrain.library.infrastructure.data.EmailManager method) get_enhanced_config_manager() (in module nanobrain.core.config.enhanced_config_manager) get_enhanced_status() (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent method) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent method) (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent method) (nanobrain.library.agents.EnhancedCollaborativeAgent method) (nanobrain.library.EnhancedCollaborativeAgent method), [1] get_error_message() (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig method) (nanobrain.core.guards.NanobrainTriggerGuardConfig method) get_execution_order() (nanobrain.core.workflow.WorkflowGraph method) (nanobrain.core.WorkflowGraph method), [1] get_export_statistics() (nanobrain.library.infrastructure.data.export_manager.ExportManager method) (nanobrain.library.infrastructure.data.ExportManager method) (nanobrain.library.infrastructure.ExportManager method) get_extraction_statistics() (nanobrain.library.agents.specialized.virus_extraction_agent.VirusExtractionAgent method) (nanobrain.library.agents.specialized.VirusExtractionAgent method) get_fasta_header() (nanobrain.core.bioinformatics.SequenceRegion method) (nanobrain.core.SequenceRegion method), [1] get_file_info() (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin method) get_format_settings() (nanobrain.library.interfaces.web.BaseFormatConverter method) (nanobrain.library.interfaces.web.processing.BaseFormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.BaseFormatConverter method) get_framework_info() (nanobrain.core.config.config_manager.ConfigManager method) get_frontend_config() (in module nanobrain.library.interfaces.web.api.frontend_router) get_guard_scope() (nanobrain.core.guards.nanobrain_guard_mixin.TriggerGuardMixin method) (nanobrain.core.guards.TriggerGuardMixin method) get_guard_status() (nanobrain.core.guards.nanobrain_guard_mixin.TriggerGuardMixin method) (nanobrain.core.guards.TriggerGuardMixin method) get_health_status() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.FormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverter method) (nanobrain.library.interfaces.web.processing.FormatConverter method) (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.StreamingHandler method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRouter method) get_healthy_processors() (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer method) (nanobrain.library.infrastructure.load_balancing.LoadBalancer method) (nanobrain.library.infrastructure.LoadBalancer method) get_historical_performance() (nanobrain.library.interfaces.web.BaseRoutingStrategy method) (nanobrain.library.interfaces.web.routing.BaseRoutingStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.BaseRoutingStrategy method) get_ictv_standards() (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusSpecificCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.VirusSpecificCacheManager method)

get_input() (nanobrain.library.infrastructure.BaseCLI method) (nanobrain.library.infrastructure.interfaces.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.base_cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.BaseCLI method) get_last_message() (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData method) (nanobrain.library.infrastructure.data.ChatSessionData method) get_link() (nanobrain.core.Workflow method), [1] (nanobrain.core.workflow.Workflow method) (nanobrain.core.workflow.WorkflowGraph method) (nanobrain.core.WorkflowGraph method), [1] get_load_distribution() (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer method) (nanobrain.library.infrastructure.load_balancing.LoadBalancer method) (nanobrain.library.infrastructure.LoadBalancer method) get_log_file_config() (nanobrain.core.config.config_manager.ConfigManager method) get_logger() (in module nanobrain.core), [1] (in module nanobrain.core.logging_system) (nanobrain.core.async_logging.AsyncLoggerFactory class method) (nanobrain.core.logging_system.SystemLogManager method) get_logging_config() (in module nanobrain.core.config.config_manager) (nanobrain.core.config.config_manager.ConfigManager method) get_logging_mode() (in module nanobrain.core.config.config_manager) (nanobrain.core.config.config_manager.ConfigManager method) get_logging_status() (in module nanobrain.core.logging_system) get_mcp_servers() (nanobrain.core.mcp_support.MCPSupportMixin method) get_mcp_status() (nanobrain.core.mcp_support.MCPSupportMixin method) get_mcp_tools() (nanobrain.core.mcp_support.MCPSupportMixin method) get_metadata() (nanobrain.core.data_unit.DataUnitBase method) (nanobrain.core.DataUnitBase method), [1] (nanobrain.library.infrastructure.DataUnitBase method) get_method_guard_scope() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_enforcer_meta) get_metric_history() (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor method) (nanobrain.library.infrastructure.PerformanceMonitor method) get_metric_statistics() (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor method) (nanobrain.library.infrastructure.PerformanceMonitor method) get_nested_value() (in module nanobrain.core.link) get_next_processor() (nanobrain.library.infrastructure.steps.parallel_step.ProcessorPool method) (nanobrain.library.infrastructure.steps.ProcessorPool method) get_object_info() (nanobrain.core.data_unit.DataUnit method) get_original_method() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_enforcer_meta) get_output() (nanobrain.core.BaseStep method), [1] (nanobrain.core.step.BaseStep method) get_parallel_execution_levels() (nanobrain.core.workflow.WorkflowGraph method) (nanobrain.core.WorkflowGraph method), [1] get_parsl_stats() (nanobrain.library.workflows.ParslChatWorkflow method) get_pattern_type_weight() (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.DomainClassifier method) get_performance_metrics() (nanobrain.library.agents.specialized.parsl_agent.ParslAgent method) (nanobrain.library.agents.specialized.ParslAgent method) get_performance_stats() (nanobrain.core.Agent method), [1] (nanobrain.core.agent.Agent method) (nanobrain.core.BaseStep method), [1] (nanobrain.core.step.BaseStep method) (nanobrain.library.infrastructure.ParallelAgentStep method) (nanobrain.library.infrastructure.ParallelConversationalAgentStep method) (nanobrain.library.infrastructure.ParallelStep method) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentStep method) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentStep method) (nanobrain.library.infrastructure.steps.parallel_step.ParallelStep method) (nanobrain.library.infrastructure.steps.ParallelAgentStep method) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentStep method) (nanobrain.library.infrastructure.steps.ParallelStep method) (nanobrain.library.ParallelAgentStep method), [1] (nanobrain.library.ParallelConversationalAgentStep method), [1] (nanobrain.library.workflows.ParslChatWorkflow method) get_performance_summary() (nanobrain.core.agent_logging.AgentLogger method) (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent method) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent method) (nanobrain.library.agents.EnhancedCollaborativeAgent method) (nanobrain.library.EnhancedCollaborativeAgent method), [1] (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer method) (nanobrain.library.infrastructure.load_balancing.LoadBalancer method) (nanobrain.library.infrastructure.LoadBalancer method) (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor method) (nanobrain.library.infrastructure.PerformanceMonitor method) get_port_mappings() (nanobrain.library.infrastructure.docker.container_config.ContainerConfig method) get_process_safe_logger() (in module nanobrain.core.async_logging) get_processor_stats() (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer method) (nanobrain.library.infrastructure.load_balancing.LoadBalancer method) (nanobrain.library.infrastructure.LoadBalancer method) get_progress() (nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow.WebProgressTracker method) (nanobrain.library.workflows.viral_protein_analysis.web.WebProgressTracker method) get_progress_history() (nanobrain.core.Workflow method), [1] (nanobrain.core.workflow.Workflow method) get_progress_summary() (nanobrain.core.Workflow method), [1] (nanobrain.core.workflow.ProgressReporter method) (nanobrain.core.workflow.Workflow method) get_prompt() (nanobrain.core.Agent method), [1] (nanobrain.core.agent.Agent method) (nanobrain.core.prompt_template_manager.PromptTemplateManager method) (nanobrain.core.PromptTemplateManager method), [1] get_prompt_info() (nanobrain.core.prompt_template_manager.PromptTemplateManager method) (nanobrain.core.PromptTemplateManager method), [1] get_protected_method_wrapper() (nanobrain.core.guards.trigger_integration.TriggerGuardIntegration static method) (nanobrain.core.guards.TriggerGuardIntegration static method) get_protected_methods() (nanobrain.core.guards.nanobrain_guard_mixin.TriggerGuardMixin method) (nanobrain.core.guards.TriggerGuardMixin method) get_provider_config() (in module nanobrain.core.config.config_manager) (nanobrain.core.config.config_manager.ConfigManager method), [1] get_recent_conversations() (nanobrain.library.ConversationHistoryUnit method), [1] (nanobrain.library.infrastructure.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.conversation_history.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.ConversationHistoryUnit method) get_recommended_scale_progression() (nanobrain.core.progressive_scaling.ProgressiveScalingMixin method) get_resource_summary() (nanobrain.core.resource_monitor.ResourceMonitor method) (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitor method) (nanobrain.library.infrastructure.monitoring.ResourceMonitor method) get_result() (nanobrain.core.BaseStep method), [1] (nanobrain.core.step.BaseStep method) get_result_enum() (nanobrain.core.testing.test_constants.TestConstants method) (nanobrain.core.testing.TestConstants method) get_rule() (nanobrain.library.agents.enhanced.delegation_engine.DelegationEngine method) get_rules() (nanobrain.library.agents.enhanced.delegation_engine.DelegationEngine method) get_scale_info() (nanobrain.core.progressive_scaling.ProgressiveScalingMixin method) get_schema() (nanobrain.core.config.config_base.ConfigBase class method) (nanobrain.core.config.ConfigBase class method) (nanobrain.core.config.schema_generator.SchemaGenerator method), [1] (nanobrain.core.LangChainTool method), [1] (nanobrain.core.mcp_support.MCPTool method) (nanobrain.core.tool.LangChainTool method) (nanobrain.core.tool.ToolBase method) (nanobrain.core.ToolBase method), [1] get_schema_with_examples() (nanobrain.core.config.config_base.ConfigBase class method) (nanobrain.core.config.ConfigBase class method) get_schemas() (nanobrain.core.tool.ToolRegistry method) (nanobrain.core.ToolRegistry method), [1] get_sequence_stats() (nanobrain.core.sequence_manager.SequenceManager method) (nanobrain.core.SequenceManager method), [1] get_server_class() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory class method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory class method) (nanobrain.library.interfaces.web.UniversalServerFactory class method) get_server_health() (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) get_service_config() (nanobrain.library.infrastructure.data.email_manager.EmailManager method) (nanobrain.library.infrastructure.data.EmailManager method) get_service_description() (nanobrain.library.infrastructure.data.email_manager.EmailManager method) (nanobrain.library.infrastructure.data.EmailManager method) get_session() (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.SessionManager method) get_session_data() (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.SessionManager method) get_session_info() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamSession method) (nanobrain.library.interfaces.web.processing.StreamSession method) (nanobrain.library.interfaces.web.StreamSession method) get_session_statistics() (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.SessionManager method) get_specialized_performance_stats() (nanobrain.library.agents.specialized.base.SpecializedAgentBase method), [1] (nanobrain.library.agents.specialized.SpecializedAgentBase method), [1] (nanobrain.library.agents.SpecializedAgentBase method), [1] get_state() (nanobrain.library.infrastructure.CircuitBreaker method) (nanobrain.library.infrastructure.load_balancing.circuit_breaker.CircuitBreaker method) (nanobrain.library.infrastructure.load_balancing.CircuitBreaker method) get_statistics() (nanobrain.library.agents.enhanced.delegation_engine.DelegationEngine method) (nanobrain.library.ConversationHistoryUnit method), [1] (nanobrain.library.infrastructure.CircuitBreaker method) (nanobrain.library.infrastructure.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.conversation_history.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.ConversationHistoryUnit method) (nanobrain.library.infrastructure.load_balancing.circuit_breaker.CircuitBreaker method) (nanobrain.library.infrastructure.load_balancing.CircuitBreaker method) (nanobrain.library.infrastructure.load_balancing.request_queue.RequestQueue method) (nanobrain.library.infrastructure.load_balancing.RequestQueue method) (nanobrain.library.infrastructure.RequestQueue method) get_stats() (nanobrain.core.workflow.WorkflowGraph method) (nanobrain.core.WorkflowGraph method), [1] (nanobrain.library.infrastructure.steps.parallel_step.ProcessorPool method) (nanobrain.library.infrastructure.steps.ProcessorPool method) get_status() (in module nanobrain.library.interfaces.web.api.health_router) (nanobrain.core.guards.examples.protected_step_example.ProtectedStepExample method) (nanobrain.library.interfaces.web.web_interface.WebInterface method) (nanobrain.library.interfaces.web.WebInterface method) (nanobrain.library.interfaces.WebInterface method) get_step() (nanobrain.core.Workflow method), [1] (nanobrain.core.workflow.Workflow method) (nanobrain.core.workflow.WorkflowGraph method) (nanobrain.core.WorkflowGraph method), [1] get_step_config() (nanobrain.core.config.yaml_config.YAMLWorkflowConfig method) get_step_dependencies() (nanobrain.core.workflow.WorkflowGraph method) (nanobrain.core.WorkflowGraph method), [1] get_step_dependents() (nanobrain.core.workflow.WorkflowGraph method) (nanobrain.core.WorkflowGraph method), [1] get_step_guard() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_trigger_guard) get_step_info() (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingStep method) get_stream_chunks() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) get_stream_iterator() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) get_stream_session() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) get_stream_statistics() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) get_supported_conversions() (nanobrain.library.interfaces.web.FormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverter method) (nanobrain.library.interfaces.web.processing.FormatConverter method) get_supported_domains() (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.DomainClassifier method) get_supported_intents() (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifier method) (nanobrain.library.interfaces.web.analysis.IntentClassifier method) (nanobrain.library.interfaces.web.IntentClassifier method) get_synonym_groups() (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusSpecificCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.VirusSpecificCacheManager method) get_system_info() (in module nanobrain.library.interfaces.web.api.frontend_router) get_system_log_manager() (in module nanobrain.core.logging_system) get_task() (nanobrain.core.a2a_support.A2AClient method) get_taxon_info() (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.VirusNameResolver method) get_template_configuration() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory class method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory class method) (nanobrain.library.interfaces.web.UniversalServerFactory class method) get_timeout_config() (nanobrain.library.infrastructure.data.email_manager.EmailManager method) (nanobrain.library.infrastructure.data.EmailManager method) get_tool() (nanobrain.core.BaseStep method), [1] (nanobrain.core.step.BaseStep method) (nanobrain.library.agents.specialized.base.BaseAgent method) get_tool_call_history() (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] get_tool_card() (nanobrain.core.card_schemas.CardManager method) get_trend_analysis() (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor method) (nanobrain.library.infrastructure.PerformanceMonitor method) get_trigger_wrapped_methods() (in module nanobrain.core.guards) (in module nanobrain.core.guards.trigger_integration) get_user_sessions() (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.SessionManager method) get_version() (nanobrain.core.external_tool.ExternalTool method) get_via_trigger_wrapper() (nanobrain.core.guards.nanobrain_guard_mixin.TriggerGuardMixin method) (nanobrain.core.guards.TriggerGuardMixin method) get_virus_cache_directory() (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusSpecificCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.VirusSpecificCacheManager method) get_virus_cache_stats() (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusSpecificCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.VirusSpecificCacheManager method) get_volume_mappings() (nanobrain.library.infrastructure.docker.container_config.ContainerConfig method) get_web_interface() (in module nanobrain.library.interfaces.web.api.frontend_router) (in module nanobrain.library.interfaces.web.api.health_router) get_workflow_config_path() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) get_workflow_guard() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_trigger_guard) get_workflow_instance() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) get_workflow_stats() (nanobrain.core.Workflow method), [1] (nanobrain.core.workflow.Workflow method) get_workflow_status() (nanobrain.library.ChatWorkflow method), [1] (nanobrain.library.workflows.ChatWorkflow method) (nanobrain.library.workflows.ParslChatWorkflow method) git_repository (nanobrain.core.external_tool.ExternalToolConfig attribute) goodbye_message (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) graph (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.Workflow attribute) GRAPH_BASED (nanobrain.core.ExecutionStrategy attribute), [1] (nanobrain.core.workflow.ExecutionStrategy attribute)

H

HALF_OPEN (nanobrain.library.infrastructure.CircuitBreakerState attribute) (nanobrain.library.infrastructure.load_balancing.circuit_breaker.CircuitBreakerState attribute) (nanobrain.library.infrastructure.load_balancing.CircuitBreakerState attribute) handle_chat_request() (in module nanobrain.library.interfaces.web.api.websocket_router) handle_multi_domain_result() (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.DomainClassifier method) handle_multi_workflow_route() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) handle_output() (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStep method) (nanobrain.library.infrastructure.interfaces.cli.CLIStep method) (nanobrain.library.infrastructure.interfaces.CLIStep method) handle_single_domain_result() (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.DomainClassifier method) handle_stream_error() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) handle_websocket_message() (in module nanobrain.library.interfaces.web.api.websocket_router) handle_workflow_command() (in module nanobrain.library.interfaces.web.api.websocket_router) handle_workflow_events (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIStepConfig attribute) handler (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) has_cycles() (nanobrain.core.workflow.WorkflowGraph method) (nanobrain.core.WorkflowGraph method), [1] has_prompt_template() (nanobrain.core.Agent method), [1] (nanobrain.core.agent.Agent method) health_check (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) health_check() (in module nanobrain.library.interfaces.web.api.health_router) (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase method)

health_check_interval (nanobrain.library.infrastructure.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) HealthCheckConfig (class in nanobrain.library.infrastructure.docker.container_config) HealthChecker (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.monitoring) (class in nanobrain.library.infrastructure.monitoring.health_checker) HealthResponse (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.response_models) hidden (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) HIGH (nanobrain.library.infrastructure.load_balancing.request_queue.RequestPriority attribute) (nanobrain.library.infrastructure.load_balancing.RequestPriority attribute) (nanobrain.library.infrastructure.RequestPriority attribute) history (nanobrain.core.a2a_support.A2ATask attribute) history_size (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor attribute) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor attribute) (nanobrain.library.infrastructure.PerformanceMonitor attribute) host (nanobrain.library.infrastructure.interfaces.database.DatabaseConfig attribute) (nanobrain.library.interfaces.web.BaseServerConfig attribute) (nanobrain.library.interfaces.web.config.web_interface_config.ServerConfig attribute) (nanobrain.library.interfaces.web.servers.base_server.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.universal_server.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.servers.UniversalServerConfig attribute) hostname (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute)

I

ictv_cache_dir (nanobrain.library.agents.specialized.protein_synonym_agent.ProteinSynonymAgent attribute) (nanobrain.library.agents.specialized.ProteinSynonymAgent attribute) ictv_cache_ttl_days (nanobrain.library.agents.specialized.protein_synonym_agent.ProteinSynonymAgent attribute) (nanobrain.library.agents.specialized.ProteinSynonymAgent attribute) id (nanobrain.core.a2a_support.A2ASkill attribute) (nanobrain.core.a2a_support.A2ATask attribute) (nanobrain.core.card_schemas.Skill attribute) (nanobrain.core.config.enhanced_config.A2ASkill attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.AgentRequest attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatRequest attribute) (nanobrain.library.infrastructure.steps.parallel_step.ProcessingRequest attribute) (nanobrain.library.infrastructure.steps.ProcessingRequest attribute) identify_domain_async() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) identify_synonyms() (nanobrain.library.agents.specialized.protein_synonym_agent.ProteinSynonymAgent method) (nanobrain.library.agents.specialized.ProteinSynonymAgent method) image (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) import_class_from_path() (in module nanobrain.core), [1] (in module nanobrain.core.component_base) import_data() (nanobrain.library.infrastructure.data.export_manager.ExportManager method) (nanobrain.library.infrastructure.data.ExportManager method) (nanobrain.library.infrastructure.ExportManager method) import_rules() (nanobrain.library.agents.enhanced.delegation_engine.DelegationEngine method) import_sessions() (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.SessionManager method) import_workflow_class() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) include_metadata (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) include_protein_types (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.EEEVAnalysisRequest attribute) incompatibility_issues (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.WorkflowCompatibilityScore attribute) indent_size (nanobrain.library.infrastructure.interfaces.cli.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.FormatterConfig attribute) index (nanobrain.core.a2a_support.A2AArtifact attribute) indicators (nanobrain.library.interfaces.web.DomainClassification attribute) (nanobrain.library.interfaces.web.models.DomainClassification attribute) (nanobrain.library.interfaces.web.models.universal_models.DomainClassification attribute) indices (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) INFO (nanobrain.core.logging_system.LogLevel attribute) (nanobrain.core.LogLevel attribute), [1] (nanobrain.library.infrastructure.data.chat_session_data.MessageType attribute) (nanobrain.library.infrastructure.data.MessageType attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.MessageType attribute) info() (nanobrain.core.async_logging.ProcessSafeLogger method) (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] INFORMATION_REQUEST (nanobrain.library.interfaces.web.IntentType attribute) (nanobrain.library.interfaces.web.models.IntentType attribute) (nanobrain.library.interfaces.web.models.universal_models.IntentType attribute) ingress_enabled (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) ingress_host (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) initial_confidence (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.CSVMatchCandidate attribute) initial_scale_level (nanobrain.core.external_tool.ExternalToolConfig attribute) initial_value (nanobrain.core.data_unit.DataUnitConfig attribute) (nanobrain.core.DataUnitConfig attribute), [1] (nanobrain.DataUnitConfig attribute) initialize() (nanobrain.core.a2a_support.A2AClient method) (nanobrain.core.Agent method), [1] (nanobrain.core.agent.Agent method) (nanobrain.core.BaseStep method), [1] (nanobrain.core.bioinformatics.BioinformaticsAgent method) (nanobrain.core.bioinformatics.BioinformaticsStep method) (nanobrain.core.bioinformatics.BioinformaticsTool method) (nanobrain.core.BioinformaticsAgent method), [1] (nanobrain.core.BioinformaticsStep method), [1] (nanobrain.core.BioinformaticsTool method), [1] (nanobrain.core.data_unit.DataUnitBase method) (nanobrain.core.data_unit.DataUnitStream method) (nanobrain.core.DataUnitBase method), [1] (nanobrain.core.DataUnitStream method), [1] (nanobrain.core.executor.ExecutorBase method) (nanobrain.core.executor.LocalExecutor method) (nanobrain.core.executor.ParslExecutor method) (nanobrain.core.executor.ProcessExecutor method) (nanobrain.core.executor.ThreadExecutor method) (nanobrain.core.ExecutorBase method), [1] (nanobrain.core.LocalExecutor method), [1] (nanobrain.core.mcp_support.MCPClient method) (nanobrain.core.ParslExecutor method), [1] (nanobrain.core.ProcessExecutor method), [1] (nanobrain.core.step.BaseStep method) (nanobrain.core.ThreadExecutor method), [1] (nanobrain.core.tool.ToolBase method) (nanobrain.core.ToolBase method), [1] (nanobrain.core.Workflow method), [1] (nanobrain.core.workflow.Workflow method) (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent method) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent method) (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent method) (nanobrain.library.agents.EnhancedCollaborativeAgent method) (nanobrain.library.agents.specialized.base.SpecializedAgentBase method), [1] (nanobrain.library.agents.specialized.parsl_agent.ParslAgent method) (nanobrain.library.agents.specialized.ParslAgent method) (nanobrain.library.agents.specialized.SpecializedAgentBase method), [1] (nanobrain.library.agents.SpecializedAgentBase method), [1] (nanobrain.library.ChatWorkflow method), [1] (nanobrain.library.EnhancedCollaborativeAgent method), [1] (nanobrain.library.infrastructure.BaseCLI method) (nanobrain.library.infrastructure.DataUnitBase method) (nanobrain.library.infrastructure.DataUnitStream method) (nanobrain.library.infrastructure.InteractiveCLI method) (nanobrain.library.infrastructure.interfaces.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.base_cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStep method) (nanobrain.library.infrastructure.interfaces.cli.CLIStep method) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.cli.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLI method) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLI method) (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.cli.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.cli.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.CLIStep method) (nanobrain.library.infrastructure.interfaces.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.InteractiveCLI method) (nanobrain.library.infrastructure.interfaces.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.ResponseFormatter method) (nanobrain.library.infrastructure.ParallelAgentStep method) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentStep method) (nanobrain.library.infrastructure.steps.ParallelAgentStep method) (nanobrain.library.interfaces.web.web_interface.WebInterface method) (nanobrain.library.interfaces.web.WebInterface method) (nanobrain.library.interfaces.WebInterface method) (nanobrain.library.ParallelAgentStep method), [1] (nanobrain.library.workflows.ChatWorkflow method) (nanobrain.library.workflows.ParslChatWorkflow method) (nanobrain.library.workflows.viral_protein_analysis.alphavirus_workflow.AlphavirusWorkflow method) (nanobrain.library.workflows.viral_protein_analysis.AlphavirusWorkflow method) (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.protein_synonym_agent_step.ProteinSynonymAgentStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.ProteinSynonymAgentStep method) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneViralProteinInterface method) (nanobrain.LocalExecutor method) (nanobrain.ParslExecutor method) initialize_a2a() (nanobrain.core.a2a_support.A2ASupportMixin method) initialize_agents_for_langchain() (in module nanobrain.core.agent) initialize_all() (nanobrain.core.tool.ToolRegistry method) (nanobrain.core.ToolRegistry method), [1] initialize_component_loading() (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) initialize_config() (in module nanobrain.core.config.config_manager) initialize_mcp() (nanobrain.core.mcp_support.MCPSupportMixin method) initialize_middleware() (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.universal_server.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.servers.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.UniversalNanoBrainServer method) initialize_session() (nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow.WebProgressTracker method) (nanobrain.library.workflows.viral_protein_analysis.web.WebProgressTracker method) initialize_steps() (nanobrain.core.workflow.ProgressReporter method) initialize_virus_index() (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.VirusNameResolver method) input (nanobrain.core.agent.AgentToolSchema attribute) (nanobrain.core.card_schemas.UsageExample attribute) input_configs (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.StepConfig attribute) input_data (nanobrain.library.infrastructure.steps.AgentRequest attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.AgentRequest attribute) input_data_units (nanobrain.core.BaseStep attribute), [1] (nanobrain.core.step.BaseStep attribute) (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.StepConfig attribute) input_encoding (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute)

input_example (nanobrain.core.config.enhanced_config.UsageExample attribute) input_format (nanobrain.core.config.enhanced_config.AgentCardSection attribute) (nanobrain.core.config.enhanced_config.ToolCardSection attribute) input_key (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIStepConfig attribute) input_length (nanobrain.core.agent_logging.AgentInteractionLog attribute) input_modes (nanobrain.core.card_schemas.Skill attribute) (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.core.config.enhanced_config.A2ASkill attribute) INPUT_REQUIRED (nanobrain.core.a2a_support.TaskStatus attribute) input_schema (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.ToolCard attribute) input_text (nanobrain.core.agent_logging.AgentInteractionLog attribute) (nanobrain.core.AgentConversationLog attribute), [1] (nanobrain.core.logging_system.AgentConversationLog attribute) input_timeout (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) input_types (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) InputMode (class in nanobrain.core.card_schemas) inputModes (nanobrain.core.a2a_support.A2ASkill attribute) InputOutputFormat (class in nanobrain.core.config.enhanced_config) InputType (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.workflow_models) install_if_missing() (nanobrain.core.external_tool.ExternalTool method) installation_path (nanobrain.core.external_tool.ExternalToolConfig attribute) (nanobrain.core.external_tool.InstallationStatus attribute) installation_status (nanobrain.core.external_tool.DiagnosticReport attribute) installation_type (nanobrain.core.external_tool.InstallationStatus attribute) InstallationStatus (class in nanobrain.core.external_tool) INTEGER (nanobrain.core.card_schemas.ParameterType attribute) (nanobrain.core.config.schema_validator.FieldType attribute) integrate_trigger_with_guards() (in module nanobrain.core.guards) (in module nanobrain.core.guards.trigger_integration) intent (nanobrain.library.infrastructure.data.chat_session_data.QueryClassificationData attribute) (nanobrain.library.infrastructure.data.QueryClassificationData attribute) intent_classification (nanobrain.library.interfaces.web.models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.models.universal_models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.RequestAnalysis attribute) intent_classifier (nanobrain.library.agents.specialized.query_analysis_agent.QueryAnalysisAgent attribute) (nanobrain.library.agents.specialized.QueryAnalysisAgent attribute) (nanobrain.library.interfaces.web.analysis.request_analyzer.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.analysis.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.RequestAnalyzerConfig attribute) intent_patterns (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.IntentClassifierConfig attribute) intent_type (nanobrain.library.interfaces.web.IntentClassification attribute) (nanobrain.library.interfaces.web.models.IntentClassification attribute) (nanobrain.library.interfaces.web.models.universal_models.IntentClassification attribute) IntentClassification (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.universal_models) IntentClassifier (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.analysis) (class in nanobrain.library.interfaces.web.analysis.intent_classifier) IntentClassifierConfig (class in nanobrain.library.interfaces.web.analysis) (class in nanobrain.library.interfaces.web.analysis.intent_classifier) IntentType (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.universal_models) interaction_context() (nanobrain.core.agent_logging.AgentLogger method) interaction_modes (nanobrain.core.card_schemas.AgentCard attribute) interaction_patterns (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) interaction_preference (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.WorkflowRequirements attribute) InteractionMetrics (class in nanobrain.library.infrastructure.data.chat_session_data) InteractionPattern (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.workflow_models) INTERACTIVE (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIMode attribute) interactive_in_workflow (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIStepConfig attribute) InteractiveCLI (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.cli) (class in nanobrain.library.infrastructure.interfaces.cli.interactive_cli) InteractiveCLIConfig (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.cli) (class in nanobrain.library.infrastructure.interfaces.cli.interactive_cli) interval (nanobrain.library.infrastructure.docker.container_config.HealthCheckConfig attribute) invalidate_service_cache() (nanobrain.library.infrastructure.data.cache_manager.CacheManager method) (nanobrain.library.infrastructure.data.CacheManager method) IOSchema (class in nanobrain.core.card_schemas) is_accepted (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.CSVMatchCandidate attribute) is_active (nanobrain.core.link.LinkBase property) (nanobrain.core.LinkBase property), [1] (nanobrain.core.trigger.TriggerBase attribute) (nanobrain.core.trigger.TriggerBase property) (nanobrain.core.TriggerBase attribute), [1] (nanobrain.core.TriggerBase property), [1] is_agent_trigger_active() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_trigger_guard) is_annotation_request (nanobrain.library.infrastructure.data.chat_session_data.QueryClassificationData property) (nanobrain.library.infrastructure.data.QueryClassificationData property) is_complete (nanobrain.library.infrastructure.data.chat_session_data.ChatMessage attribute) (nanobrain.library.infrastructure.data.ChatMessage attribute) is_connected (nanobrain.core.link.LinkBase attribute) (nanobrain.core.LinkBase attribute), [1] is_conversational_request (nanobrain.library.infrastructure.data.chat_session_data.QueryClassificationData property) (nanobrain.library.infrastructure.data.QueryClassificationData property) is_conversion_supported() (nanobrain.library.interfaces.web.FormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverter method) (nanobrain.library.interfaces.web.processing.FormatConverter method) is_development_mode() (nanobrain.core.config.config_manager.ConfigManager method) is_empty() (nanobrain.library.infrastructure.load_balancing.request_queue.RequestQueue method) (nanobrain.library.infrastructure.load_balancing.RequestQueue method) (nanobrain.library.infrastructure.RequestQueue method) is_expired (nanobrain.library.infrastructure.data.AnnotationJobData property) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData property) (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData property) (nanobrain.library.infrastructure.data.ChatSessionData property) is_expired() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamSession method) (nanobrain.library.interfaces.web.processing.StreamSession method) (nanobrain.library.interfaces.web.StreamSession method) is_failure() (nanobrain.core.testing.test_constants.TestConstants method) (nanobrain.core.testing.TestConstants method) is_final (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.StreamingResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StreamingResponse attribute) (nanobrain.library.interfaces.web.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.StreamingResponse attribute) is_full() (nanobrain.library.infrastructure.load_balancing.request_queue.RequestQueue method) (nanobrain.library.infrastructure.load_balancing.RequestQueue method) (nanobrain.library.infrastructure.RequestQueue method) is_initialized (nanobrain.core.Agent property), [1] (nanobrain.core.agent.Agent property) (nanobrain.core.BaseStep property), [1] (nanobrain.core.data_unit.DataUnitBase property) (nanobrain.core.DataUnitBase property), [1] (nanobrain.core.executor.ExecutorBase attribute) (nanobrain.core.executor.ExecutorBase property) (nanobrain.core.ExecutorBase attribute), [1] (nanobrain.core.ExecutorBase property), [1] (nanobrain.core.step.BaseStep property) (nanobrain.core.tool.ToolBase property) (nanobrain.core.ToolBase property), [1] (nanobrain.library.infrastructure.DataUnitBase property) is_method_protected() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_enforcer_meta) (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig method) (nanobrain.core.guards.nanobrain_guard_mixin.TriggerGuardMixin method) (nanobrain.core.guards.NanobrainTriggerGuardConfig method) (nanobrain.core.guards.TriggerGuardMixin method) is_running (nanobrain.core.BaseStep property), [1] (nanobrain.core.step.BaseStep property) is_session_valid() (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.SessionManager method) is_step_trigger_active() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_trigger_guard) is_streaming (nanobrain.library.infrastructure.data.chat_session_data.ChatMessage attribute) (nanobrain.library.infrastructure.data.ChatMessage attribute) is_success() (nanobrain.core.testing.test_constants.TestConstants method) (nanobrain.core.testing.TestConstants method) is_trigger_active() (in module nanobrain.core.guards) (in module nanobrain.core.guards.contextvar_core) (nanobrain.core.guards.nanobrain_trigger_guard.NanobrainTriggerGuard method) (nanobrain.core.guards.NanobrainTriggerGuard method) is_trigger_currently_active() (nanobrain.core.guards.nanobrain_guard_mixin.TriggerGuardMixin method) (nanobrain.core.guards.TriggerGuardMixin method) is_trigger_guard_aware() (in module nanobrain.core.guards) (in module nanobrain.core.guards.trigger_integration) is_unknown_request (nanobrain.library.infrastructure.data.chat_session_data.QueryClassificationData property) (nanobrain.library.infrastructure.data.QueryClassificationData property) is_valid (nanobrain.library.infrastructure.interfaces.cli.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.CLIContext attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.WorkflowValidationResult attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.ValidationResult attribute) is_workflow_class() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) is_workflow_trigger_active() (in module nanobrain.core.guards) (in module nanobrain.core.guards.nanobrain_trigger_guard) issues (nanobrain.core.external_tool.InstallationStatus attribute) IUPAC_DNA (nanobrain.core.sequence_manager.SequenceValidator attribute) (nanobrain.core.SequenceValidator attribute), [1] IUPAC_RNA (nanobrain.core.sequence_manager.SequenceValidator attribute) (nanobrain.core.SequenceValidator attribute), [1]

J

job_id (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) JSON (nanobrain.core.card_schemas.InputMode attribute) (nanobrain.core.card_schemas.OutputMode attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.OutputFormat attribute) JSON_DATA (nanobrain.library.interfaces.web.models.OutputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.OutputType attribute) (nanobrain.library.interfaces.web.OutputType attribute)

json_indent (nanobrain.library.infrastructure.interfaces.cli.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.FormatterConfig attribute) json_sort_keys (nanobrain.library.infrastructure.interfaces.cli.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.FormatterConfig attribute) JSONConverter (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.processing) (class in nanobrain.library.interfaces.web.processing.format_converter)

K

keyword_based_config (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.IntentClassifierConfig attribute) keywords (nanobrain.library.agents.enhanced.delegation_engine.DelegationRule attribute) (nanobrain.library.interfaces.web.IntentClassification attribute) (nanobrain.library.interfaces.web.models.IntentClassification attribute) (nanobrain.library.interfaces.web.models.universal_models.IntentClassification attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute)

KUBERNETES (nanobrain.library.infrastructure.docker.container_config.ContainerOrchestrator attribute)

L

labels (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) (nanobrain.library.infrastructure.docker.container_config.DockerComponentConfig attribute) LANGCHAIN (nanobrain.core.tool.ToolType attribute) (nanobrain.core.ToolType attribute), [1] LangChainTool (class in nanobrain.core), [1] (class in nanobrain.core.tool) language_patterns (nanobrain.library.agents.specialized.code_writer.CodeWriterAgentMixin attribute) last_accessed (nanobrain.library.infrastructure.data.session_manager.SessionData attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.WorkflowRegistryEntry attribute) last_activity (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData attribute) (nanobrain.library.infrastructure.data.ChatSessionData attribute) last_error (nanobrain.library.interfaces.web.models.response_models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.WorkflowStatusResponse attribute) last_message_time (nanobrain.library.interfaces.web.api.frontend_router.ConversationSummary attribute) last_trigger_time (nanobrain.core.trigger.TriggerBase attribute) (nanobrain.core.TriggerBase attribute), [1] last_updated (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.core.workflow.WorkflowProgress attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) lastChunk (nanobrain.core.a2a_support.A2AArtifact attribute) LEAST_LOADED (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.load_balancing.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.steps.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.steps.parallel_step.LoadBalancingStrategy attribute) length (nanobrain.core.sequence_manager.SequenceStats attribute) (nanobrain.core.SequenceStats attribute), [1] length() (nanobrain.core.bioinformatics.SequenceCoordinate method) (nanobrain.core.SequenceCoordinate method), [1] level (nanobrain.core.async_logging.LogMessage attribute) license (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.ToolCard attribute) LIGHT (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLITheme attribute) limitations (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.ToolCard attribute) link_type (nanobrain.core.link.LinkBase attribute) (nanobrain.core.link.LinkConfig attribute) (nanobrain.core.LinkBase attribute), [1] (nanobrain.core.LinkConfig attribute), [1] (nanobrain.LinkConfig attribute) LinkBase (class in nanobrain.core), [1] (class in nanobrain.core.link) LinkConfig (class in nanobrain) (class in nanobrain.core), [1] (class in nanobrain.core.link) links (nanobrain.core.config.yaml_config.YAMLWorkflowConfig attribute) (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.Workflow attribute) (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] LinkType (class in nanobrain.core), [1] (class in nanobrain.core.link) LIST (nanobrain.core.config.schema_validator.FieldType attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.OutputFormat attribute) list_agent_cards() (nanobrain.core.card_schemas.CardManager method) list_available_tools() (nanobrain.library.agents.specialized.base.BaseAgent method) list_commands() (nanobrain.library.infrastructure.interfaces.cli.command_processor.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.cli.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.CommandProcessor method) list_contexts() (nanobrain.core.prompt_template_manager.PromptTemplateManager method) (nanobrain.core.PromptTemplateManager method), [1] list_directory() (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin method) list_links() (nanobrain.core.Workflow method), [1] (nanobrain.core.workflow.Workflow method) list_prompts() (nanobrain.core.prompt_template_manager.PromptTemplateManager method) (nanobrain.core.PromptTemplateManager method), [1] list_schemas() (nanobrain.core.config.schema_generator.SchemaGenerator method) list_steps() (nanobrain.core.Workflow method), [1] (nanobrain.core.workflow.Workflow method) list_tool_cards() (nanobrain.core.card_schemas.CardManager method) list_tools() (nanobrain.core.BaseStep method), [1] (nanobrain.core.step.BaseStep method) (nanobrain.core.tool.ToolRegistry method) (nanobrain.core.ToolRegistry method), [1] LLM_CALL (nanobrain.core.logging_system.OperationType attribute) (nanobrain.core.OperationType attribute), [1] llm_calls (nanobrain.core.agent_logging.AgentInteractionLog attribute) (nanobrain.core.AgentConversationLog attribute), [1] (nanobrain.core.logging_system.AgentConversationLog attribute) llm_config (nanobrain.core.config.enhanced_config.EnhancedAgentConfig attribute) load_a2a_config_from_file() (nanobrain.core.a2a_support.A2ASupportMixin method) load_a2a_config_from_yaml() (in module nanobrain.core.a2a_support) load_agent_card() (nanobrain.core.card_schemas.CardManager method) load_analysis_components() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) LOAD_BALANCER (nanobrain.library.infrastructure.docker.container_config.ServiceType attribute) load_balancing_strategy (nanobrain.library.infrastructure.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) load_component_via_framework() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) load_components_from_config() (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) load_config() (in module nanobrain.core.config.yaml_config) (nanobrain.core.config.config_manager.ConfigManager method), [1] (nanobrain.library.interfaces.web.config.ConfigurationManager static method) load_config_file() (in module nanobrain.core.config.component_factory) load_docker_config() (in module nanobrain.library.interfaces.web.config) load_enhanced_agent_config() (nanobrain.core.config.enhanced_config_manager.EnhancedConfigManager method) load_enhanced_tool_config() (nanobrain.core.config.enhanced_config_manager.EnhancedConfigManager method) load_mcp_config_from_file() (nanobrain.core.mcp_support.MCPSupportMixin method) load_mcp_config_from_yaml() (in module nanobrain.core.mcp_support) load_minimal_config() (in module nanobrain.library.interfaces.web.config) load_schema_from_yaml() (nanobrain.core.config.schema_validator.SchemaValidator method)

load_sequences_from_fasta() (nanobrain.core.sequence_manager.SequenceManager method) (nanobrain.core.SequenceManager method), [1] load_server_configuration() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory class method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory class method) (nanobrain.library.interfaces.web.UniversalServerFactory class method) load_step_config() (nanobrain.core.ConfigLoader method), [1] (nanobrain.core.workflow.ConfigLoader method) load_templates() (nanobrain.core.prompt_template_manager.PromptTemplateManager method) (nanobrain.core.PromptTemplateManager method), [1] load_tool_card() (nanobrain.core.card_schemas.CardManager method) load_universal_config() (in module nanobrain.library.interfaces.web.config) load_workflow_config() (nanobrain.core.ConfigLoader method), [1] (nanobrain.core.workflow.ConfigLoader method) LoadBalancer (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.load_balancing) (class in nanobrain.library.infrastructure.load_balancing.load_balancer) LoadBalancingStrategy (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.load_balancing) (class in nanobrain.library.infrastructure.load_balancing.load_balancer) (class in nanobrain.library.infrastructure.steps) (class in nanobrain.library.infrastructure.steps.parallel_step) loading_context (nanobrain.core.config.config_base.ConfigBase attribute) (nanobrain.core.config.ConfigBase attribute) loading_timestamp (nanobrain.core.config.config_base.ConfigLoadingContext attribute) LOCAL (nanobrain.core.executor.ExecutorType attribute) local_installation_paths (nanobrain.core.external_tool.ExternalToolConfig attribute) LocalExecutor (class in nanobrain) (class in nanobrain.core), [1] (class in nanobrain.core.executor) log_agent_calls (nanobrain.core.a2a_support.A2AClientConfig attribute) log_agent_conversation() (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] log_commands (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) log_component_lifecycle() (in module nanobrain.core.logging_system) (nanobrain.core.logging_system.SystemLogManager method) log_conversations (nanobrain.AgentConfig attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] log_data_transfer() (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] log_data_transfers (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.StepConfig attribute) log_data_unit_operation() (in module nanobrain.core.logging_system) (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.logging_system.SystemLogManager method) (nanobrain.core.NanoBrainLogger method), [1] log_debug() (nanobrain.core.agent_logging.AgentLogger method) log_error() (nanobrain.core.agent_logging.AgentLogger method) log_executions (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.StepConfig attribute) log_guard_events (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig attribute) log_interaction() (nanobrain.core.agent_logging.AgentLogger method) log_level (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) (nanobrain.library.interfaces.web.config.web_interface_config.LoggingConfig attribute) log_lifecycle_event() (nanobrain.core.agent_logging.AgentLogger method) log_link_operation() (in module nanobrain.core.logging_system) (nanobrain.core.logging_system.SystemLogManager method) log_llm_call() (nanobrain.core.agent_logging.AgentLogger method) log_operation() (nanobrain.library.infrastructure.data.data_unit_logger.DataUnitLogger method) log_requests_body (nanobrain.library.interfaces.web.config.web_interface_config.LoggingConfig attribute) log_responses_body (nanobrain.library.interfaces.web.config.web_interface_config.LoggingConfig attribute) log_step_execution() (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] log_tool_call() (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] log_tool_calls (nanobrain.AgentConfig attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.core.mcp_support.MCPClientConfig attribute) log_trigger_activation() (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] log_trigger_event() (in module nanobrain.core.logging_system) (nanobrain.core.logging_system.SystemLogManager method) log_user_input (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) log_workflow_event() (in module nanobrain.core.logging_system) (nanobrain.core.logging_system.SystemLogManager method) logger (nanobrain.library.infrastructure.CircuitBreaker attribute) (nanobrain.library.infrastructure.load_balancing.circuit_breaker.CircuitBreaker attribute) (nanobrain.library.infrastructure.load_balancing.CircuitBreaker attribute) (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer attribute) (nanobrain.library.infrastructure.load_balancing.LoadBalancer attribute) (nanobrain.library.infrastructure.LoadBalancer attribute) (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor attribute) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor attribute) (nanobrain.library.infrastructure.PerformanceMonitor attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.EnhancedBVBRCDataAcquisitionStep attribute) logger_name (nanobrain.core.async_logging.LogMessage attribute) logging (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig attribute) (nanobrain.library.interfaces.web.WebInterfaceConfig attribute) (nanobrain.library.interfaces.WebInterfaceConfig attribute) LoggingConfig (class in nanobrain.library.interfaces.web.config.web_interface_config) LoggingMiddleware (class in nanobrain.library.interfaces.web.middleware) (class in nanobrain.library.interfaces.web.middleware.logging_middleware) LogLevel (class in nanobrain.core), [1] (class in nanobrain.core.logging_system) LogMessage (class in nanobrain.core.async_logging) LOW (nanobrain.library.infrastructure.load_balancing.request_queue.RequestPriority attribute) (nanobrain.library.infrastructure.load_balancing.RequestPriority attribute) (nanobrain.library.infrastructure.RequestPriority attribute)

M

main() (in module nanobrain.library.interfaces.web.chatbot_server) (in module nanobrain.library.interfaces.web.demo_server) (in module nanobrain.library.interfaces.web.web_interface) MANUAL (nanobrain.core.trigger.TriggerType attribute) (nanobrain.core.TriggerType attribute), [1] ManualTrigger (class in nanobrain.core), [1] (class in nanobrain.core.trigger) map_domain_name_to_enum() (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.DomainClassifier method) map_intent_name_to_enum() (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifier method) (nanobrain.library.interfaces.web.analysis.IntentClassifier method) (nanobrain.library.interfaces.web.IntentClassifier method) mark_complete() (nanobrain.library.infrastructure.data.chat_session_data.ChatMessage method) (nanobrain.library.infrastructure.data.ChatMessage method) mark_completed() (nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow.WebProgressTracker method) (nanobrain.library.workflows.viral_protein_analysis.web.WebProgressTracker method) mark_error() (nanobrain.library.infrastructure.data.chat_session_data.ChatMessage method) (nanobrain.library.infrastructure.data.ChatMessage method) mark_failed() (nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow.WebProgressTracker method) (nanobrain.library.workflows.viral_protein_analysis.web.WebProgressTracker method) mark_last_message_complete() (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData method) (nanobrain.library.infrastructure.data.ChatSessionData method) mark_last_message_error() (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData method) (nanobrain.library.infrastructure.data.ChatSessionData method) match_method (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.CSVMatchCandidate attribute) match_reasons (nanobrain.library.interfaces.web.models.universal_models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.WorkflowMatch attribute) match_score (nanobrain.library.interfaces.web.models.universal_models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.WorkflowMatch attribute) match_type (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.TaxonResolution attribute) matched_name (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.TaxonResolution attribute) MAX (nanobrain.core.config.schema_validator.ConstraintType attribute) max_args (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) max_batch_size (nanobrain.library.infrastructure.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) max_concurrent_sessions (nanobrain.core.config.enhanced_config.PerformanceSpec attribute) max_concurrent_streams (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.processing.StreamingHandlerConfig attribute) max_context_length (nanobrain.core.card_schemas.AgentCard attribute) max_conversation_length (nanobrain.library.interfaces.web.config.web_interface_config.ChatConfig attribute) max_frequency_hz (nanobrain.core.trigger.TriggerBase attribute) (nanobrain.core.trigger.TriggerConfig attribute) (nanobrain.core.TriggerBase attribute), [1] (nanobrain.core.TriggerConfig attribute), [1] (nanobrain.TriggerConfig attribute) MAX_LENGTH (nanobrain.core.config.schema_validator.ConstraintType attribute) max_line_length (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.FormatterConfig attribute) max_message_length (nanobrain.library.infrastructure.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) max_parallel_requests (nanobrain.library.infrastructure.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) max_parallel_steps (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] max_processing_time (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowRequirements attribute) max_products_per_request (nanobrain.library.agents.specialized.protein_synonym_agent.ProteinSynonymAgent attribute) (nanobrain.library.agents.specialized.ProteinSynonymAgent attribute) max_replicas (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) max_response_time (nanobrain.core.config.enhanced_config.PerformanceSpec attribute) max_retries (nanobrain.core.a2a_support.A2AAgentConfig attribute) (nanobrain.core.config.config_manager.ProviderConfig attribute) (nanobrain.core.config.enhanced_config.EnhancedToolConfig attribute) (nanobrain.core.mcp_support.MCPServerConfig attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) max_species_candidates (nanobrain.library.agents.specialized.virus_extraction_agent.VirusExtractionAgent attribute) (nanobrain.library.agents.specialized.VirusExtractionAgent attribute) max_tokens (nanobrain.AgentConfig attribute) (nanobrain.core.Agent attribute), [1] (nanobrain.core.agent.Agent attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.library.interfaces.web.ChatOptions attribute) (nanobrain.library.interfaces.web.models.ChatOptions attribute) (nanobrain.library.interfaces.web.models.request_models.ChatOptions attribute) max_value (nanobrain.core.card_schemas.ParameterSchema attribute) max_workers (nanobrain.core.executor.ExecutorBase attribute) (nanobrain.core.executor.ExecutorConfig attribute) (nanobrain.core.ExecutorBase attribute), [1] (nanobrain.core.ExecutorConfig attribute), [1] (nanobrain.ExecutorConfig attribute) mcp_config (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent attribute) mcp_config_path (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) (nanobrain.library.EnhancedCollaborativeAgent attribute), [1] mcp_server_name (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) mcp_server_url (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) mcp_support (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.core.bioinformatics.BioinformaticsConfig attribute) (nanobrain.core.config.config_base.ConfigBase attribute) (nanobrain.core.config.ConfigBase attribute) (nanobrain.core.config.yaml_config.YAMLConfig attribute) (nanobrain.core.data_unit.DataUnitConfig attribute) (nanobrain.core.DataUnitConfig attribute), [1] (nanobrain.core.executor.ExecutorConfig attribute) (nanobrain.core.ExecutorConfig attribute), [1] (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig attribute) (nanobrain.core.link.LinkConfig attribute) (nanobrain.core.LinkConfig attribute), [1] (nanobrain.core.prompt_template_manager.PromptTemplateConfig attribute) (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.testing.test_result_config.TestResultConfig attribute) (nanobrain.core.tool.ToolConfig attribute) (nanobrain.core.trigger.TriggerConfig attribute) (nanobrain.core.TriggerConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.request_analyzer.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.analysis.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverterConfig attribute) (nanobrain.library.interfaces.web.processing.FormatConverterConfig attribute) (nanobrain.library.interfaces.web.processing.response_processor.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.processing.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.routing.routing_strategies.RoutingStrategyConfig attribute) (nanobrain.library.interfaces.web.routing.RoutingStrategyConfig attribute) (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.servers.base_server.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.server_factory.ServerFactoryConfig attribute) (nanobrain.library.interfaces.web.servers.ServerFactoryConfig attribute) (nanobrain.library.interfaces.web.servers.universal_server.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.servers.UniversalServerConfig attribute) mcp_tools (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) MCPAuthenticationError MCPClient (class in nanobrain.core.mcp_support) MCPClientConfig (class in nanobrain.core.mcp_support) MCPConfigurationError MCPConnectionError MCPError MCPServerConfig (class in nanobrain.core.mcp_support) MCPSupportMixin (class in nanobrain.core.mcp_support) MCPTool (class in nanobrain.core.mcp_support) MCPToolExecutionError MCPToolInfo (class in nanobrain.core.mcp_support) mem_limit (nanobrain.library.infrastructure.docker.container_config.ResourceLimits attribute) memory (nanobrain.library.infrastructure.docker.container_config.ResourceLimits attribute) memory_config (nanobrain.core.config.enhanced_config.EnhancedAgentConfig attribute) memory_critical_percentage (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitorConfig attribute) (nanobrain.library.infrastructure.monitoring.ResourceMonitorConfig attribute) memory_request (nanobrain.library.infrastructure.docker.container_config.ResourceLimits attribute) memory_usage (nanobrain.core.card_schemas.PerformanceMetrics attribute) (nanobrain.core.config.enhanced_config.PerformanceSpec attribute) memory_warning_percentage (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitorConfig attribute) (nanobrain.library.infrastructure.monitoring.ResourceMonitorConfig attribute) MemoryInfo (class in nanobrain.library.infrastructure.monitoring) (class in nanobrain.library.infrastructure.monitoring.resource_monitor) merge_configs() (nanobrain.library.interfaces.web.config.ConfigurationManager static method) merge_configurations() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory class method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory class method) (nanobrain.library.interfaces.web.UniversalServerFactory class method) merge_regions() (nanobrain.core.sequence_manager.SequenceManager method) (nanobrain.core.SequenceManager method), [1] merge_templates() (nanobrain.core.prompt_template_manager.PromptTemplateManager method) (nanobrain.core.PromptTemplateManager method), [1] merge_with() (nanobrain.core.config.yaml_config.YAMLConfig method) (nanobrain.core.config.YAMLConfig method) message (nanobrain.core.a2a_support.A2ATaskStatus attribute) (nanobrain.core.async_logging.LogMessage attribute) (nanobrain.core.config.schema_validator.FieldConstraint attribute) (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) (nanobrain.library.infrastructure.steps.ChatRequest attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatRequest attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendChatRequest attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.api.FrontendChatRequest attribute) (nanobrain.library.interfaces.web.api.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.api.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.FrontendChatRequest attribute) (nanobrain.library.interfaces.web.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.StandardizedResponse attribute) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.AnalysisProgress attribute) message_count (nanobrain.library.interfaces.web.api.frontend_router.ConversationSummary attribute) message_id (nanobrain.library.infrastructure.data.chat_session_data.ChatMessage attribute) (nanobrain.library.infrastructure.data.ChatMessage attribute) (nanobrain.library.infrastructure.data.conversation_history.ConversationMessage attribute) (nanobrain.library.infrastructure.data.ConversationMessage attribute) (nanobrain.library.interfaces.web.api.websocket_router.WebSocketMessage attribute) message_type (nanobrain.library.infrastructure.data.chat_session_data.ChatMessage attribute) (nanobrain.library.infrastructure.data.ChatMessage attribute) MessageQueueInterface (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.external) MessageRole (class in nanobrain.library.infrastructure.data) (class in nanobrain.library.infrastructure.data.chat_session_data) messages (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData attribute) (nanobrain.library.infrastructure.data.ChatSessionData attribute) MessageType (class in nanobrain.library.infrastructure.data) (class in nanobrain.library.infrastructure.data.chat_session_data) (class in nanobrain.library.infrastructure.interfaces.cli.response_formatter) (class in nanobrain.library.interfaces.web.api.websocket_router) metadata (nanobrain.core.a2a_support.A2AArtifact attribute) (nanobrain.core.a2a_support.A2AMessage attribute) (nanobrain.core.a2a_support.A2APart attribute) (nanobrain.core.a2a_support.A2ATask attribute) (nanobrain.core.agent_logging.AgentInteractionLog attribute) (nanobrain.core.async_logging.LogMessage attribute) (nanobrain.core.data_unit.DataUnitBase attribute) (nanobrain.core.data_unit.DataUnitBase property) (nanobrain.core.DataUnitBase attribute), [1] (nanobrain.core.DataUnitBase property), [1] (nanobrain.core.ExecutionContext attribute), [1] (nanobrain.core.logging_system.ExecutionContext attribute) (nanobrain.library.infrastructure.data.chat_session_data.ChatMessage attribute) (nanobrain.library.infrastructure.data.ChatMessage attribute) (nanobrain.library.infrastructure.data.conversation_history.ConversationMessage attribute) (nanobrain.library.infrastructure.data.ConversationMessage attribute) (nanobrain.library.infrastructure.data.session_manager.SessionData attribute) (nanobrain.library.infrastructure.DataUnitBase attribute) (nanobrain.library.infrastructure.DataUnitBase property) (nanobrain.library.infrastructure.load_balancing.request_queue.QueuedRequest attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.AgentResponse attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatResponse attribute) (nanobrain.library.infrastructure.steps.parallel_step.ProcessingResponse attribute) (nanobrain.library.infrastructure.steps.ProcessingResponse attribute) (nanobrain.library.interfaces.web.AggregatedResponse attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.api.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.ChatOptions attribute) (nanobrain.library.interfaces.web.ChatResponse attribute) (nanobrain.library.interfaces.web.DomainClassification attribute) (nanobrain.library.interfaces.web.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.IntentClassification attribute) (nanobrain.library.interfaces.web.models.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.ChatOptions attribute) (nanobrain.library.interfaces.web.models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.DomainClassification attribute) (nanobrain.library.interfaces.web.models.IntentClassification attribute) (nanobrain.library.interfaces.web.models.request_models.ChatOptions attribute) (nanobrain.library.interfaces.web.models.response_models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.models.StreamingResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.DomainClassification attribute) (nanobrain.library.interfaces.web.models.universal_models.IntentClassification attribute) (nanobrain.library.interfaces.web.models.universal_models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StreamingResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.StandardizedResponse attribute) (nanobrain.library.interfaces.web.StreamingResponse attribute) (nanobrain.library.interfaces.web.UniversalResponse attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowMatch attribute) (nanobrain.library.interfaces.web.WorkflowRegistryEntry attribute) method (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.IntentClassifierConfig attribute) metrics (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData attribute) (nanobrain.library.infrastructure.data.ChatSessionData attribute) (nanobrain.library.interfaces.web.models.response_models.StatusResponse attribute) (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusCacheEntry attribute) metrics_history (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor attribute) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor attribute) (nanobrain.library.infrastructure.PerformanceMonitor attribute) MetricsDashboard (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.monitoring) (class in nanobrain.library.infrastructure.monitoring.metrics_dashboard) middleware (nanobrain.library.interfaces.web.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.base_server.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.universal_server.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.servers.UniversalServerConfig attribute) MIN (nanobrain.core.config.schema_validator.ConstraintType attribute) min_args (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) min_confidence (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.WorkflowRequirements attribute) min_confidence_threshold (nanobrain.library.agents.specialized.protein_synonym_agent.ProteinSynonymAgent attribute) (nanobrain.library.agents.specialized.ProteinSynonymAgent attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) MIN_LENGTH (nanobrain.core.config.schema_validator.ConstraintType attribute) min_replicas (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) min_update_interval (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) min_value (nanobrain.core.card_schemas.ParameterSchema attribute) MINIMAL (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLITheme attribute) minimum_compliance_score (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.WorkflowRegistryConfig attribute) MockA2ASession (class in nanobrain.core.a2a_support) mode (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) model (nanobrain.AgentConfig attribute) (nanobrain.core.Agent attribute), [1] (nanobrain.core.agent.Agent attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.library.interfaces.web.ChatOptions attribute) (nanobrain.library.interfaces.web.models.ChatOptions attribute) (nanobrain.library.interfaces.web.models.request_models.ChatOptions attribute) model_config (nanobrain.AgentConfig attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.agent.AgentLangChainTool attribute) (nanobrain.core.agent.AgentToolSchema attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.core.bioinformatics.BioinformaticsConfig attribute) (nanobrain.core.bioinformatics.SequenceCoordinate attribute) (nanobrain.core.bioinformatics.SequenceRegion attribute) (nanobrain.core.BioinformaticsConfig attribute), [1] (nanobrain.core.config.config_base.ConfigBase attribute), [1] (nanobrain.core.config.ConfigBase attribute), [1] (nanobrain.core.config.enhanced_config.A2ACapabilities attribute) (nanobrain.core.config.enhanced_config.A2ASkill attribute) (nanobrain.core.config.enhanced_config.AgentCardSection attribute) (nanobrain.core.config.enhanced_config.EnhancedAgentConfig attribute) (nanobrain.core.config.enhanced_config.EnhancedToolConfig attribute) (nanobrain.core.config.enhanced_config.InputOutputFormat attribute) (nanobrain.core.config.enhanced_config.PerformanceSpec attribute) (nanobrain.core.config.enhanced_config.ToolCapabilities attribute) (nanobrain.core.config.enhanced_config.ToolCardSection attribute) (nanobrain.core.config.enhanced_config.UsageExample attribute) (nanobrain.core.config.schema_validator.ConfigSchema attribute) (nanobrain.core.config.schema_validator.FieldConstraint attribute) (nanobrain.core.config.schema_validator.FieldSchema attribute) (nanobrain.core.config.schema_validator.ParameterSchema attribute) (nanobrain.core.config.schema_validator.ValidatorFunction attribute) (nanobrain.core.config.yaml_config.YAMLConfig attribute), [1] (nanobrain.core.config.yaml_config.YAMLWorkflowConfig attribute) (nanobrain.core.config.YAMLConfig attribute), [1] (nanobrain.core.data_unit.DataUnitConfig attribute) (nanobrain.core.DataUnitConfig attribute), [1] (nanobrain.core.executor.ExecutorConfig attribute) (nanobrain.core.ExecutorConfig attribute), [1] (nanobrain.core.external_tool.ExternalToolConfig attribute) (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig attribute) (nanobrain.core.guards.nanobrain_trigger_guard.TriggerGuardConfig attribute) (nanobrain.core.guards.NanobrainTriggerGuardConfig attribute) (nanobrain.core.link.LinkConfig attribute) (nanobrain.core.LinkConfig attribute), [1] (nanobrain.core.prompt_template_manager.PromptTemplate attribute) (nanobrain.core.prompt_template_manager.PromptTemplateConfig attribute) (nanobrain.core.PromptTemplate attribute), [1] (nanobrain.core.PromptTemplateConfig attribute), [1] (nanobrain.core.resource_monitor.ResourceMonitorConfig attribute) (nanobrain.core.SequenceCoordinate attribute), [1] (nanobrain.core.SequenceRegion attribute), [1] (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.testing.test_result_config.TestResultConfig attribute) (nanobrain.core.testing.TestResultConfig attribute) (nanobrain.core.tool.ToolConfig attribute) (nanobrain.core.ToolConfig attribute), [1] (nanobrain.core.trigger.TriggerConfig attribute) (nanobrain.core.TriggerConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] (nanobrain.DataUnitConfig attribute) (nanobrain.ExecutorConfig attribute) (nanobrain.library.infrastructure.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.library.interfaces.web.AggregatedResponse attribute) (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.IntentClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.request_analyzer.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.analysis.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.api.frontend_router.ConversationSummary attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendChatRequest attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.api.frontend_router.SystemInfo attribute) (nanobrain.library.interfaces.web.api.FrontendChatRequest attribute) (nanobrain.library.interfaces.web.api.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.api.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.api.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.BaseServerConfig attribute) (nanobrain.library.interfaces.web.ChatOptions attribute) (nanobrain.library.interfaces.web.ChatRequest attribute) (nanobrain.library.interfaces.web.ChatResponse attribute) (nanobrain.library.interfaces.web.DomainClassification attribute) (nanobrain.library.interfaces.web.ErrorResponse attribute) (nanobrain.library.interfaces.web.FormatConverterConfig attribute) (nanobrain.library.interfaces.web.FrontendChatRequest attribute) (nanobrain.library.interfaces.web.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.HealthResponse attribute) (nanobrain.library.interfaces.web.IntentClassification attribute) (nanobrain.library.interfaces.web.models.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.ChatOptions attribute) (nanobrain.library.interfaces.web.models.ChatRequest attribute) (nanobrain.library.interfaces.web.models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.DomainClassification attribute) (nanobrain.library.interfaces.web.models.ErrorResponse attribute) (nanobrain.library.interfaces.web.models.HealthResponse attribute) (nanobrain.library.interfaces.web.models.IntentClassification attribute) (nanobrain.library.interfaces.web.models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.models.request_models.ChatOptions attribute) (nanobrain.library.interfaces.web.models.request_models.ChatRequest attribute) (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.models.response_models.ChatMetadata attribute) (nanobrain.library.interfaces.web.models.response_models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.response_models.ErrorResponse attribute) (nanobrain.library.interfaces.web.models.response_models.HealthResponse attribute) (nanobrain.library.interfaces.web.models.response_models.StatusResponse attribute) (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.response_models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.StreamingResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.DomainClassification attribute) (nanobrain.library.interfaces.web.models.universal_models.IntentClassification attribute) (nanobrain.library.interfaces.web.models.universal_models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.models.universal_models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.models.universal_models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StreamingResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.models.universal_models.WorkflowRoute attribute) (nanobrain.library.interfaces.web.models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.models.WorkflowRoute attribute) (nanobrain.library.interfaces.web.models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverterConfig attribute) (nanobrain.library.interfaces.web.processing.FormatConverterConfig attribute) (nanobrain.library.interfaces.web.processing.response_processor.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.processing.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.RequestAnalysis attribute) (nanobrain.library.interfaces.web.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.routing.routing_strategies.RoutingStrategyConfig attribute) (nanobrain.library.interfaces.web.routing.RoutingStrategyConfig attribute) (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.RoutingStrategyConfig attribute) (nanobrain.library.interfaces.web.ServerFactoryConfig attribute) (nanobrain.library.interfaces.web.servers.base_server.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.server_factory.ServerFactoryConfig attribute) (nanobrain.library.interfaces.web.servers.ServerFactoryConfig attribute) (nanobrain.library.interfaces.web.servers.universal_server.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.servers.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.StandardizedResponse attribute) (nanobrain.library.interfaces.web.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.StreamingResponse attribute) (nanobrain.library.interfaces.web.UniversalResponse attribute) (nanobrain.library.interfaces.web.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.WorkflowMatch attribute) (nanobrain.library.interfaces.web.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.WorkflowRoute attribute) (nanobrain.library.interfaces.web.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.WorkflowValidationResult attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.EEEVAnalysisRequest attribute) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneConfig attribute) (nanobrain.LinkConfig attribute) (nanobrain.StepConfig attribute) (nanobrain.TriggerConfig attribute)

model_pools (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent attribute) model_post_init() (nanobrain.core.config.config_base.ConfigBase method) (nanobrain.core.config.ConfigBase method) model_used (nanobrain.library.interfaces.web.models.response_models.ChatMetadata attribute) module nanobrain nanobrain.core, [1] nanobrain.core.a2a_support nanobrain.core.agent nanobrain.core.agent_logging nanobrain.core.async_logging nanobrain.core.bioinformatics nanobrain.core.card_schemas nanobrain.core.component_base nanobrain.core.config nanobrain.core.config.component_factory nanobrain.core.config.config_base nanobrain.core.config.config_manager nanobrain.core.config.enhanced_config nanobrain.core.config.enhanced_config_manager nanobrain.core.config.schema_generator nanobrain.core.config.schema_validator nanobrain.core.config.yaml_config nanobrain.core.data_unit nanobrain.core.executor nanobrain.core.external_tool nanobrain.core.guards nanobrain.core.guards.contextvar_core nanobrain.core.guards.examples.protected_step_example nanobrain.core.guards.nanobrain_enforcer_meta nanobrain.core.guards.nanobrain_guard_config nanobrain.core.guards.nanobrain_guard_mixin nanobrain.core.guards.nanobrain_trigger_guard nanobrain.core.guards.trigger_integration nanobrain.core.link nanobrain.core.logging_system nanobrain.core.mcp_support nanobrain.core.progressive_scaling nanobrain.core.prompt_template_manager nanobrain.core.resource_monitor nanobrain.core.sequence_manager nanobrain.core.step nanobrain.core.testing nanobrain.core.testing.test_constants nanobrain.core.testing.test_result_config nanobrain.core.tool nanobrain.core.trigger nanobrain.core.workflow nanobrain.library, [1] nanobrain.library.agents nanobrain.library.agents.conversational nanobrain.library.agents.conversational.enhanced_collaborative_agent nanobrain.library.agents.enhanced.collaborative_agent nanobrain.library.agents.enhanced.delegation_engine nanobrain.library.agents.specialized nanobrain.library.agents.specialized.base nanobrain.library.agents.specialized.code_writer nanobrain.library.agents.specialized.file_writer nanobrain.library.agents.specialized.parsl_agent nanobrain.library.agents.specialized.protein_synonym_agent nanobrain.library.agents.specialized.query_analysis_agent nanobrain.library.agents.specialized.virus_extraction_agent nanobrain.library.bioinformatics nanobrain.library.infrastructure nanobrain.library.infrastructure.data nanobrain.library.infrastructure.data.cache_manager nanobrain.library.infrastructure.data.chat_session_data nanobrain.library.infrastructure.data.conversation_history nanobrain.library.infrastructure.data.data_unit_logger nanobrain.library.infrastructure.data.email_manager nanobrain.library.infrastructure.data.export_manager nanobrain.library.infrastructure.data.session_manager nanobrain.library.infrastructure.docker.container_config nanobrain.library.infrastructure.interfaces nanobrain.library.infrastructure.interfaces.cli nanobrain.library.infrastructure.interfaces.cli.base_cli nanobrain.library.infrastructure.interfaces.cli.cli_step nanobrain.library.infrastructure.interfaces.cli.command_processor nanobrain.library.infrastructure.interfaces.cli.interactive_cli nanobrain.library.infrastructure.interfaces.cli.progress_indicator nanobrain.library.infrastructure.interfaces.cli.response_formatter nanobrain.library.infrastructure.interfaces.database nanobrain.library.infrastructure.interfaces.external nanobrain.library.infrastructure.links nanobrain.library.infrastructure.load_balancing nanobrain.library.infrastructure.load_balancing.circuit_breaker nanobrain.library.infrastructure.load_balancing.load_balancer nanobrain.library.infrastructure.load_balancing.request_queue nanobrain.library.infrastructure.monitoring nanobrain.library.infrastructure.monitoring.health_checker nanobrain.library.infrastructure.monitoring.metrics_dashboard nanobrain.library.infrastructure.monitoring.performance_monitor nanobrain.library.infrastructure.monitoring.resource_monitor nanobrain.library.infrastructure.steps nanobrain.library.infrastructure.steps.parallel_agent_step nanobrain.library.infrastructure.steps.parallel_conversational_agent_step nanobrain.library.infrastructure.steps.parallel_step nanobrain.library.infrastructure.triggers nanobrain.library.interfaces nanobrain.library.interfaces.web nanobrain.library.interfaces.web.analysis nanobrain.library.interfaces.web.analysis.domain_classifier nanobrain.library.interfaces.web.analysis.intent_classifier nanobrain.library.interfaces.web.analysis.request_analyzer nanobrain.library.interfaces.web.api nanobrain.library.interfaces.web.api.chat_router nanobrain.library.interfaces.web.api.frontend_router nanobrain.library.interfaces.web.api.health_router nanobrain.library.interfaces.web.api.websocket_router nanobrain.library.interfaces.web.chatbot_server nanobrain.library.interfaces.web.config nanobrain.library.interfaces.web.config.web_interface_config nanobrain.library.interfaces.web.demo_server nanobrain.library.interfaces.web.frontend nanobrain.library.interfaces.web.middleware nanobrain.library.interfaces.web.middleware.cors_middleware nanobrain.library.interfaces.web.middleware.logging_middleware nanobrain.library.interfaces.web.models nanobrain.library.interfaces.web.models.request_models nanobrain.library.interfaces.web.models.response_models nanobrain.library.interfaces.web.models.universal_models nanobrain.library.interfaces.web.models.workflow_models nanobrain.library.interfaces.web.processing nanobrain.library.interfaces.web.processing.format_converter nanobrain.library.interfaces.web.processing.response_processor nanobrain.library.interfaces.web.processing.streaming_handler nanobrain.library.interfaces.web.routing nanobrain.library.interfaces.web.routing.routing_strategies nanobrain.library.interfaces.web.routing.workflow_registry nanobrain.library.interfaces.web.routing.workflow_router nanobrain.library.interfaces.web.servers nanobrain.library.interfaces.web.servers.base_server nanobrain.library.interfaces.web.servers.server_factory nanobrain.library.interfaces.web.servers.universal_server nanobrain.library.interfaces.web.web_interface nanobrain.library.workflows nanobrain.library.workflows.conversational nanobrain.library.workflows.conversational.viral_expert_workflow nanobrain.library.workflows.viral_protein_analysis nanobrain.library.workflows.viral_protein_analysis.alphavirus_workflow nanobrain.library.workflows.viral_protein_analysis.base_cache_manager nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline nanobrain.library.workflows.viral_protein_analysis.steps nanobrain.library.workflows.viral_protein_analysis.steps.alignment_step nanobrain.library.workflows.viral_protein_analysis.steps.annotation_mapping_step nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step nanobrain.library.workflows.viral_protein_analysis.steps.clustering_step nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step nanobrain.library.workflows.viral_protein_analysis.steps.data_aggregation_step nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step nanobrain.library.workflows.viral_protein_analysis.steps.protein_synonym_agent_step nanobrain.library.workflows.viral_protein_analysis.steps.pssm_analysis_step nanobrain.library.workflows.viral_protein_analysis.steps.result_collection_step nanobrain.library.workflows.viral_protein_analysis.steps.sequence_curation_step nanobrain.library.workflows.viral_protein_analysis.steps.viral_pssm_generation_step nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager nanobrain.library.workflows.viral_protein_analysis.web nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow MongoDBAdapter (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.database) MongoDBConfig (class in nanobrain.library.infrastructure.interfaces.database) monitoring_enabled (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.Workflow attribute) monitoring_interval_seconds (nanobrain.core.resource_monitor.ResourceMonitorConfig attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitorConfig attribute) (nanobrain.library.infrastructure.monitoring.ResourceMonitorConfig attribute) monitoring_paths (nanobrain.core.resource_monitor.ResourceMonitorConfig attribute) multi_turn_conversation (nanobrain.core.card_schemas.AgentCapabilities attribute) (nanobrain.core.config.enhanced_config.A2ACapabilities attribute) MULTI_WORKFLOW (nanobrain.library.interfaces.web.models.RoutingStrategy attribute) (nanobrain.library.interfaces.web.models.universal_models.RoutingStrategy attribute) (nanobrain.library.interfaces.web.RoutingStrategy attribute) MultiCriteriaStrategy (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.routing) (class in nanobrain.library.interfaces.web.routing.routing_strategies) MULTIPART (nanobrain.core.card_schemas.InputMode attribute) MultiWorkflowRoute (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.universal_models) MySQLAdapter (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.database) MySQLConfig (class in nanobrain.library.infrastructure.interfaces.database)

N

n_count (nanobrain.core.sequence_manager.SequenceStats attribute) (nanobrain.core.SequenceStats attribute), [1] name (nanobrain.AgentConfig attribute) (nanobrain.core.a2a_support.A2AAgentCard attribute) (nanobrain.core.a2a_support.A2AAgentConfig attribute) (nanobrain.core.a2a_support.A2AArtifact attribute) (nanobrain.core.a2a_support.A2ASkill attribute) (nanobrain.core.Agent attribute), [1] (nanobrain.core.agent.Agent attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.core.BaseStep attribute), [1] (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.ParameterSchema attribute) (nanobrain.core.card_schemas.Skill attribute) (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.core.card_schemas.UsageExample attribute) (nanobrain.core.config.enhanced_config.A2ASkill attribute) (nanobrain.core.config.enhanced_config.EnhancedAgentConfig attribute) (nanobrain.core.config.enhanced_config.EnhancedToolConfig attribute) (nanobrain.core.config.enhanced_config.UsageExample attribute) (nanobrain.core.config.schema_validator.ConfigSchema attribute) (nanobrain.core.config.schema_validator.FieldSchema attribute) (nanobrain.core.config.schema_validator.ValidatorFunction attribute) (nanobrain.core.config.yaml_config.YAMLWorkflowConfig attribute) (nanobrain.core.data_unit.DataUnitBase attribute) (nanobrain.core.data_unit.DataUnitConfig attribute) (nanobrain.core.DataUnitBase attribute), [1] (nanobrain.core.DataUnitConfig attribute), [1] (nanobrain.core.executor.ExecutorBase attribute) (nanobrain.core.ExecutorBase attribute), [1] (nanobrain.core.link.LinkBase attribute) (nanobrain.core.LinkBase attribute), [1] (nanobrain.core.mcp_support.MCPServerConfig attribute) (nanobrain.core.mcp_support.MCPToolInfo attribute) (nanobrain.core.step.BaseStep attribute) (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.tool.ToolBase attribute) (nanobrain.core.tool.ToolConfig attribute) (nanobrain.core.ToolBase attribute), [1] (nanobrain.core.ToolConfig attribute), [1] (nanobrain.core.trigger.TriggerBase attribute) (nanobrain.core.trigger.TriggerConfig attribute) (nanobrain.core.TriggerBase attribute), [1] (nanobrain.core.TriggerConfig attribute), [1] (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.ProgressStep attribute) (nanobrain.core.workflow.Workflow attribute) (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.DataUnitConfig attribute) (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) (nanobrain.library.EnhancedCollaborativeAgent attribute), [1] (nanobrain.library.infrastructure.DataUnitBase attribute) (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMetric attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig attribute) (nanobrain.library.interfaces.web.WebInterfaceConfig attribute) (nanobrain.library.interfaces.WebInterfaceConfig attribute) (nanobrain.StepConfig attribute) (nanobrain.TriggerConfig attribute) namespace (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) nanobrain module nanobrain.core module, [1] nanobrain.core.a2a_support module nanobrain.core.agent module nanobrain.core.agent_logging module nanobrain.core.async_logging module nanobrain.core.bioinformatics module nanobrain.core.card_schemas module nanobrain.core.component_base module nanobrain.core.config module nanobrain.core.config.component_factory module nanobrain.core.config.config_base module nanobrain.core.config.config_manager module nanobrain.core.config.enhanced_config module nanobrain.core.config.enhanced_config_manager module nanobrain.core.config.schema_generator module nanobrain.core.config.schema_validator module nanobrain.core.config.yaml_config module nanobrain.core.data_unit module nanobrain.core.executor module nanobrain.core.external_tool module nanobrain.core.guards module nanobrain.core.guards.contextvar_core module nanobrain.core.guards.examples.protected_step_example module nanobrain.core.guards.nanobrain_enforcer_meta module nanobrain.core.guards.nanobrain_guard_config module nanobrain.core.guards.nanobrain_guard_mixin module nanobrain.core.guards.nanobrain_trigger_guard module nanobrain.core.guards.trigger_integration module nanobrain.core.link module nanobrain.core.logging_system module nanobrain.core.mcp_support module nanobrain.core.progressive_scaling module nanobrain.core.prompt_template_manager module nanobrain.core.resource_monitor module nanobrain.core.sequence_manager module nanobrain.core.step module nanobrain.core.testing module nanobrain.core.testing.test_constants module nanobrain.core.testing.test_result_config module nanobrain.core.tool module nanobrain.core.trigger module nanobrain.core.workflow module nanobrain.library module, [1] nanobrain.library.agents module nanobrain.library.agents.conversational module nanobrain.library.agents.conversational.enhanced_collaborative_agent module nanobrain.library.agents.enhanced.collaborative_agent module nanobrain.library.agents.enhanced.delegation_engine module nanobrain.library.agents.specialized module nanobrain.library.agents.specialized.base module nanobrain.library.agents.specialized.code_writer module nanobrain.library.agents.specialized.file_writer module nanobrain.library.agents.specialized.parsl_agent module nanobrain.library.agents.specialized.protein_synonym_agent module nanobrain.library.agents.specialized.query_analysis_agent module nanobrain.library.agents.specialized.virus_extraction_agent module nanobrain.library.bioinformatics module nanobrain.library.infrastructure module nanobrain.library.infrastructure.data module nanobrain.library.infrastructure.data.cache_manager module nanobrain.library.infrastructure.data.chat_session_data module nanobrain.library.infrastructure.data.conversation_history module nanobrain.library.infrastructure.data.data_unit_logger module nanobrain.library.infrastructure.data.email_manager module nanobrain.library.infrastructure.data.export_manager module nanobrain.library.infrastructure.data.session_manager module nanobrain.library.infrastructure.docker.container_config module nanobrain.library.infrastructure.interfaces module

nanobrain.library.infrastructure.interfaces.cli module nanobrain.library.infrastructure.interfaces.cli.base_cli module nanobrain.library.infrastructure.interfaces.cli.cli_step module nanobrain.library.infrastructure.interfaces.cli.command_processor module nanobrain.library.infrastructure.interfaces.cli.interactive_cli module nanobrain.library.infrastructure.interfaces.cli.progress_indicator module nanobrain.library.infrastructure.interfaces.cli.response_formatter module nanobrain.library.infrastructure.interfaces.database module nanobrain.library.infrastructure.interfaces.external module nanobrain.library.infrastructure.links module nanobrain.library.infrastructure.load_balancing module nanobrain.library.infrastructure.load_balancing.circuit_breaker module nanobrain.library.infrastructure.load_balancing.load_balancer module nanobrain.library.infrastructure.load_balancing.request_queue module nanobrain.library.infrastructure.monitoring module nanobrain.library.infrastructure.monitoring.health_checker module nanobrain.library.infrastructure.monitoring.metrics_dashboard module nanobrain.library.infrastructure.monitoring.performance_monitor module nanobrain.library.infrastructure.monitoring.resource_monitor module nanobrain.library.infrastructure.steps module nanobrain.library.infrastructure.steps.parallel_agent_step module nanobrain.library.infrastructure.steps.parallel_conversational_agent_step module nanobrain.library.infrastructure.steps.parallel_step module nanobrain.library.infrastructure.triggers module nanobrain.library.interfaces module nanobrain.library.interfaces.web module nanobrain.library.interfaces.web.analysis module nanobrain.library.interfaces.web.analysis.domain_classifier module nanobrain.library.interfaces.web.analysis.intent_classifier module nanobrain.library.interfaces.web.analysis.request_analyzer module nanobrain.library.interfaces.web.api module nanobrain.library.interfaces.web.api.chat_router module nanobrain.library.interfaces.web.api.frontend_router module nanobrain.library.interfaces.web.api.health_router module nanobrain.library.interfaces.web.api.websocket_router module nanobrain.library.interfaces.web.chatbot_server module nanobrain.library.interfaces.web.config module nanobrain.library.interfaces.web.config.web_interface_config module nanobrain.library.interfaces.web.demo_server module nanobrain.library.interfaces.web.frontend module nanobrain.library.interfaces.web.middleware module nanobrain.library.interfaces.web.middleware.cors_middleware module nanobrain.library.interfaces.web.middleware.logging_middleware module nanobrain.library.interfaces.web.models module nanobrain.library.interfaces.web.models.request_models module nanobrain.library.interfaces.web.models.response_models module nanobrain.library.interfaces.web.models.universal_models module nanobrain.library.interfaces.web.models.workflow_models module nanobrain.library.interfaces.web.processing module nanobrain.library.interfaces.web.processing.format_converter module nanobrain.library.interfaces.web.processing.response_processor module nanobrain.library.interfaces.web.processing.streaming_handler module nanobrain.library.interfaces.web.routing module nanobrain.library.interfaces.web.routing.routing_strategies module nanobrain.library.interfaces.web.routing.workflow_registry module nanobrain.library.interfaces.web.routing.workflow_router module nanobrain.library.interfaces.web.servers module nanobrain.library.interfaces.web.servers.base_server module nanobrain.library.interfaces.web.servers.server_factory module nanobrain.library.interfaces.web.servers.universal_server module nanobrain.library.interfaces.web.web_interface module nanobrain.library.workflows module nanobrain.library.workflows.conversational module nanobrain.library.workflows.conversational.viral_expert_workflow module nanobrain.library.workflows.viral_protein_analysis module nanobrain.library.workflows.viral_protein_analysis.alphavirus_workflow module nanobrain.library.workflows.viral_protein_analysis.base_cache_manager module nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline module nanobrain.library.workflows.viral_protein_analysis.steps module nanobrain.library.workflows.viral_protein_analysis.steps.alignment_step module nanobrain.library.workflows.viral_protein_analysis.steps.annotation_mapping_step module nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step module nanobrain.library.workflows.viral_protein_analysis.steps.clustering_step module nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step module nanobrain.library.workflows.viral_protein_analysis.steps.data_aggregation_step module nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step module nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step module nanobrain.library.workflows.viral_protein_analysis.steps.protein_synonym_agent_step module nanobrain.library.workflows.viral_protein_analysis.steps.pssm_analysis_step module nanobrain.library.workflows.viral_protein_analysis.steps.result_collection_step module nanobrain.library.workflows.viral_protein_analysis.steps.sequence_curation_step module nanobrain.library.workflows.viral_protein_analysis.steps.viral_pssm_generation_step module nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration module nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver module nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager module nanobrain.library.workflows.viral_protein_analysis.web module nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface module nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow module NanobrainGuardMeta (class in nanobrain.core.guards) (class in nanobrain.core.guards.nanobrain_enforcer_meta) NanoBrainLogger (class in nanobrain.core), [1] (class in nanobrain.core.logging_system) NanobrainTriggerEnforcerMeta (class in nanobrain.core.guards) (class in nanobrain.core.guards.nanobrain_enforcer_meta) NanobrainTriggerGuard (class in nanobrain.core.guards) (class in nanobrain.core.guards.nanobrain_trigger_guard) NanobrainTriggerGuardConfig (class in nanobrain.core.guards) (class in nanobrain.core.guards.nanobrain_guard_config) natural_language_input (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) NATURAL_LANGUAGE_QUERY (nanobrain.library.interfaces.web.InputType attribute) (nanobrain.library.interfaces.web.models.InputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.InputType attribute) nb_logger (nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow.ViralAnalysisWebWorkflow attribute) (nanobrain.library.workflows.viral_protein_analysis.web.ViralAnalysisWebWorkflow attribute) networks (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) NO (nanobrain.library.infrastructure.docker.container_config.RestartPolicy attribute) NODE_PORT (nanobrain.library.infrastructure.docker.container_config.ServiceType attribute) node_selector (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) NORMAL (nanobrain.library.infrastructure.load_balancing.request_queue.RequestPriority attribute) (nanobrain.library.infrastructure.load_balancing.RequestPriority attribute) (nanobrain.library.infrastructure.RequestPriority attribute) NoSQLInterface (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.database) NoSQLQuery (class in nanobrain.library.infrastructure.interfaces.database) NoSQLQueryBuilder (class in nanobrain.library.infrastructure.interfaces.database) NoSQLResult (class in nanobrain.library.infrastructure.interfaces.database) notification_cooldown_seconds (nanobrain.core.resource_monitor.ResourceMonitorConfig attribute) notify_subscribers() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) NUCLEOTIDE (nanobrain.core.bioinformatics.SequenceType attribute) (nanobrain.core.SequenceType attribute), [1]

O

oauth_config (nanobrain.core.a2a_support.A2AAgentConfig attribute) (nanobrain.core.mcp_support.MCPServerConfig attribute) OBJECT (nanobrain.core.card_schemas.ParameterType attribute) (nanobrain.core.config.schema_validator.FieldType attribute) ON_FAILURE (nanobrain.library.infrastructure.docker.container_config.RestartPolicy attribute) ONE_BASED (nanobrain.core.bioinformatics.CoordinateSystem attribute) (nanobrain.core.CoordinateSystem attribute), [1] only_via_trigger() (in module nanobrain.core.guards) (in module nanobrain.core.guards.contextvar_core) (nanobrain.core.guards.nanobrain_trigger_guard.NanobrainTriggerGuard method) (nanobrain.core.guards.NanobrainTriggerGuard method) OPEN (nanobrain.library.infrastructure.CircuitBreakerState attribute) (nanobrain.library.infrastructure.load_balancing.circuit_breaker.CircuitBreakerState attribute) (nanobrain.library.infrastructure.load_balancing.CircuitBreakerState attribute) operation (nanobrain.core.config.schema_validator.ParameterSchema attribute) operation_type (nanobrain.core.ExecutionContext attribute), [1] (nanobrain.core.logging_system.ExecutionContext attribute) OperationType (class in nanobrain.core), [1] (class in nanobrain.core.logging_system) optional_args (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) OPTIONAL_CONFIG_FIELDS (nanobrain.core.Agent attribute), [1] (nanobrain.core.agent.Agent attribute) (nanobrain.core.BaseStep attribute), [1] (nanobrain.core.component_base.FromConfigBase attribute), [1] (nanobrain.core.ConditionalLink attribute), [1] (nanobrain.core.data_unit.DataUnitBase attribute) (nanobrain.core.DataUnitBase attribute), [1] (nanobrain.core.DirectLink attribute), [1] (nanobrain.core.executor.ExecutorBase attribute) (nanobrain.core.ExecutorBase attribute), [1] (nanobrain.core.external_tool.ExternalTool attribute) (nanobrain.core.FromConfigBase attribute), [1], [2], [3] (nanobrain.core.link.ConditionalLink attribute) (nanobrain.core.link.DirectLink attribute) (nanobrain.core.link.LinkBase attribute) (nanobrain.core.LinkBase attribute), [1] (nanobrain.core.Step attribute), [1] (nanobrain.core.step.BaseStep attribute) (nanobrain.core.step.Step attribute) (nanobrain.core.step.TransformStep attribute) (nanobrain.core.tool.ToolBase attribute) (nanobrain.core.ToolBase attribute), [1] (nanobrain.core.TransformStep attribute), [1] (nanobrain.core.trigger.TriggerBase attribute) (nanobrain.core.TriggerBase attribute), [1] (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.Workflow attribute) (nanobrain.DirectLink attribute) (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.ConversationalSpecializedAgent attribute) (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.SimpleSpecializedAgent attribute) (nanobrain.library.agents.specialized.base.BaseAgent attribute) (nanobrain.library.agents.specialized.base.ConversationalSpecializedAgent attribute) (nanobrain.library.agents.specialized.base.SimpleSpecializedAgent attribute) (nanobrain.library.agents.specialized.ConversationalSpecializedAgent attribute) (nanobrain.library.agents.specialized.SimpleSpecializedAgent attribute) (nanobrain.library.agents.specialized.virus_extraction_agent.VirusExtractionAgent attribute) (nanobrain.library.agents.specialized.VirusExtractionAgent attribute) (nanobrain.library.ChatWorkflow attribute), [1] (nanobrain.library.EnhancedCollaborativeAgent attribute), [1] (nanobrain.library.infrastructure.DataUnitBase attribute) (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase attribute) (nanobrain.library.infrastructure.docker.container_config.DockerComponentBase attribute) (nanobrain.library.interfaces.web.web_interface.WebInterface attribute) (nanobrain.library.interfaces.web.WebInterface attribute) (nanobrain.library.interfaces.WebInterface attribute) (nanobrain.library.workflows.ChatWorkflow attribute) (nanobrain.library.workflows.ParslChatWorkflow attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.data_aggregation_step.DataAggregationStep attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.DataAggregationStep attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.result_collection_step.ResultCollectionStep attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.ResultCollectionStep attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.viral_pssm_generation_step.ViralPSSMGenerationStep attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.ViralPSSMGenerationStep attribute) (nanobrain.Step attribute) optional_domains (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.WorkflowRequirements attribute)

optional_fields (nanobrain.core.config.schema_validator.ConfigSchema attribute) optional_params (nanobrain.core.prompt_template_manager.PromptTemplate attribute) (nanobrain.core.PromptTemplate attribute), [1] options (nanobrain.library.infrastructure.interfaces.cli.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.CLIContext attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendChatRequest attribute) (nanobrain.library.interfaces.web.api.FrontendChatRequest attribute) (nanobrain.library.interfaces.web.ChatRequest attribute) (nanobrain.library.interfaces.web.FrontendChatRequest attribute) (nanobrain.library.interfaces.web.models.ChatRequest attribute) (nanobrain.library.interfaces.web.models.request_models.ChatRequest attribute) (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.StreamingChatRequest attribute) organism (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.EEEVAnalysisRequest attribute) organization (nanobrain.core.a2a_support.A2AProvider attribute) original_query (nanobrain.library.infrastructure.data.chat_session_data.QueryClassificationData attribute) (nanobrain.library.infrastructure.data.QueryClassificationData attribute) (nanobrain.library.interfaces.web.models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.models.universal_models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.RequestAnalysis attribute) output_config (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.StepConfig attribute) output_data (nanobrain.library.infrastructure.steps.AgentResponse attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.AgentResponse attribute) output_data_units (nanobrain.core.BaseStep attribute), [1] (nanobrain.core.step.BaseStep attribute) (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.StepConfig attribute) output_encoding (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) output_flush_interval (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) output_format (nanobrain.core.config.enhanced_config.AgentCardSection attribute) (nanobrain.core.config.enhanced_config.ToolCardSection attribute) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.EEEVAnalysisRequest attribute) output_formatting (nanobrain.library.interfaces.web.processing.response_processor.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.ResponseProcessorConfig attribute) output_key (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIStepConfig attribute) output_modes (nanobrain.core.card_schemas.Skill attribute) (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.core.config.enhanced_config.A2ASkill attribute) output_schema (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.ToolCard attribute) output_types (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) OutputFormat (class in nanobrain.library.infrastructure.interfaces.cli.response_formatter) OutputMode (class in nanobrain.core.card_schemas) outputModes (nanobrain.core.a2a_support.A2ASkill attribute) OutputType (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.workflow_models) overall_progress (nanobrain.core.workflow.WorkflowProgress attribute) overall_score (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.WorkflowCompatibilityScore attribute) overlaps() (nanobrain.core.bioinformatics.SequenceCoordinate method) (nanobrain.core.SequenceCoordinate method), [1]

P

PARALLEL (nanobrain.core.ExecutionStrategy attribute), [1] (nanobrain.core.workflow.ExecutionStrategy attribute) ParallelAgentConfig (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.steps) (class in nanobrain.library.infrastructure.steps.parallel_agent_step) ParallelAgentStep (class in nanobrain.library), [1] (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.steps) (class in nanobrain.library.infrastructure.steps.parallel_agent_step) ParallelConversationalAgentConfig (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.steps) (class in nanobrain.library.infrastructure.steps.parallel_conversational_agent_step) ParallelConversationalAgentStep (class in nanobrain.library), [1] (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.steps) (class in nanobrain.library.infrastructure.steps.parallel_conversational_agent_step) ParallelProcessingConfig (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.steps) (class in nanobrain.library.infrastructure.steps.parallel_step) ParallelStep (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.steps) (class in nanobrain.library.infrastructure.steps.parallel_step) parameter_extractor (nanobrain.library.agents.specialized.query_analysis_agent.QueryAnalysisAgent attribute) (nanobrain.library.agents.specialized.QueryAnalysisAgent attribute) parameters (nanobrain.core.card_schemas.IOSchema attribute) (nanobrain.core.config.schema_validator.ConfigSchema attribute) (nanobrain.core.logging_system.ToolCallLog attribute) (nanobrain.core.tool.ToolBase attribute) (nanobrain.core.tool.ToolConfig attribute) (nanobrain.core.ToolBase attribute), [1] (nanobrain.core.ToolCallLog attribute), [1] (nanobrain.core.ToolConfig attribute), [1] ParameterSchema (class in nanobrain.core.card_schemas) (class in nanobrain.core.config.schema_validator) ParameterType (class in nanobrain.core.card_schemas) parent_request_id (nanobrain.core.ExecutionContext attribute), [1] (nanobrain.core.logging_system.ExecutionContext attribute) parse_condition_from_config() (in module nanobrain.core.link) parse_fasta_file() (nanobrain.core.FastaParser method), [1] (nanobrain.core.sequence_manager.FastaParser method) parse_fasta_string() (nanobrain.core.FastaParser method), [1] (nanobrain.core.sequence_manager.FastaParser method) parse_output() (nanobrain.core.external_tool.ExternalTool method) parsed_args (nanobrain.library.infrastructure.interfaces.cli.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.CLIContext attribute) PARSL (nanobrain.core.executor.ExecutorType attribute) parsl_config (nanobrain.core.executor.ExecutorConfig attribute) (nanobrain.core.ExecutorConfig attribute), [1] (nanobrain.ExecutorConfig attribute) ParslAgent (class in nanobrain.library.agents.specialized) (class in nanobrain.library.agents.specialized.parsl_agent) ParslChatWorkflow (class in nanobrain.library.workflows) ParslExecutor (class in nanobrain) (class in nanobrain.core), [1] (class in nanobrain.core.executor) PARTIAL (nanobrain.library.interfaces.web.models.response_models.ResponseStatus attribute) partial_failures (nanobrain.library.interfaces.web.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.AggregatedResponse attribute) parts (nanobrain.core.a2a_support.A2AArtifact attribute) (nanobrain.core.a2a_support.A2AMessage attribute) PartType (class in nanobrain.core.a2a_support) PASS (nanobrain.core.testing.test_constants.TestResult attribute) (nanobrain.core.testing.TestResult attribute) pass_through_data (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIStepConfig attribute) pass_value (nanobrain.core.testing.test_result_config.TestResultConfig attribute) (nanobrain.core.testing.TestResultConfig attribute) password (nanobrain.library.infrastructure.interfaces.database.DatabaseConfig attribute) path (nanobrain.core.resource_monitor.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.docker.container_config.HealthCheckConfig attribute) pattern (nanobrain.core.card_schemas.ParameterSchema attribute) PATTERN (nanobrain.core.config.schema_validator.ConstraintType attribute) pause_on_critical_disk (nanobrain.core.resource_monitor.ResourceMonitorConfig attribute) peek() (nanobrain.library.infrastructure.load_balancing.request_queue.RequestQueue method) (nanobrain.library.infrastructure.load_balancing.RequestQueue method) (nanobrain.library.infrastructure.RequestQueue method) PENDING (nanobrain.core.testing.test_constants.TestResult attribute) (nanobrain.core.testing.TestResult attribute) pending_value (nanobrain.core.testing.test_result_config.TestResultConfig attribute) (nanobrain.core.testing.TestResultConfig attribute) PERCENTAGE (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressStyle attribute) performance (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.core.config.enhanced_config.AgentCardSection attribute) (nanobrain.core.config.enhanced_config.ToolCardSection attribute) performance_config (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.IntentClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.request_analyzer.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.analysis.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.processing.response_processor.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.RequestAnalyzerConfig attribute) (nanobrain.library.interfaces.web.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.WorkflowRouterConfig attribute) performance_metrics (nanobrain.core.Agent attribute), [1] (nanobrain.core.agent.Agent attribute) (nanobrain.core.BaseStep attribute), [1] (nanobrain.core.data_unit.DataUnitBase attribute) (nanobrain.core.DataUnitBase attribute), [1] (nanobrain.core.executor.ExecutorBase attribute) (nanobrain.core.ExecutorBase attribute), [1] (nanobrain.core.link.LinkBase attribute) (nanobrain.core.LinkBase attribute), [1] (nanobrain.core.step.BaseStep attribute) (nanobrain.core.tool.ToolBase attribute) (nanobrain.core.ToolBase attribute), [1] (nanobrain.core.trigger.TriggerBase attribute) (nanobrain.core.TriggerBase attribute), [1] (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.Workflow attribute) (nanobrain.library.infrastructure.DataUnitBase attribute) (nanobrain.library.interfaces.web.models.response_models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.WorkflowStatusResponse attribute) performance_monitor (nanobrain.library.ChatWorkflow attribute), [1] (nanobrain.library.workflows.ChatWorkflow attribute) performance_tracking (nanobrain.library.infrastructure.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) PerformanceMetric (class in nanobrain.library.infrastructure.monitoring.performance_monitor) PerformanceMetrics (class in nanobrain.core.card_schemas) PerformanceMonitor (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.monitoring) (class in nanobrain.library.infrastructure.monitoring.performance_monitor) PerformanceSpec (class in nanobrain.core.config.enhanced_config) permissions_check (nanobrain.core.external_tool.DiagnosticReport attribute) persistent (nanobrain.core.data_unit.DataUnitBase attribute) (nanobrain.core.data_unit.DataUnitConfig attribute) (nanobrain.core.DataUnitBase attribute), [1] (nanobrain.core.DataUnitConfig attribute), [1] (nanobrain.DataUnitConfig attribute) (nanobrain.library.infrastructure.DataUnitBase attribute) persistent_volume_claims (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) PING (nanobrain.library.interfaces.web.api.websocket_router.MessageType attribute) ping() (in module nanobrain.library.interfaces.web.api.health_router) ping_all_connections() (nanobrain.library.interfaces.web.api.websocket_router.ConnectionManager method) pip_package (nanobrain.core.external_tool.ExternalToolConfig attribute) PipelineFiles (class in nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline) PipelineResult (class in nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline) PLAIN (nanobrain.library.infrastructure.interfaces.cli.response_formatter.OutputFormat attribute) plan_id (nanobrain.library.interfaces.web.models.workflow_models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.WorkflowExecutionPlan attribute) plan_metadata (nanobrain.library.interfaces.web.models.workflow_models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.WorkflowExecutionPlan attribute) PLUGIN (nanobrain.library.infrastructure.interfaces.cli.command_processor.CommandType attribute) plugin_directories (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) PONG (nanobrain.library.interfaces.web.api.websocket_router.MessageType attribute) port (nanobrain.library.infrastructure.docker.container_config.HealthCheckConfig attribute) (nanobrain.library.infrastructure.interfaces.database.DatabaseConfig attribute) (nanobrain.library.infrastructure.interfaces.database.MongoDBConfig attribute) (nanobrain.library.infrastructure.interfaces.database.MySQLConfig attribute) (nanobrain.library.infrastructure.interfaces.database.PostgreSQLConfig attribute) (nanobrain.library.interfaces.web.BaseServerConfig attribute) (nanobrain.library.interfaces.web.config.web_interface_config.ServerConfig attribute) (nanobrain.library.interfaces.web.servers.base_server.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.universal_server.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.servers.UniversalServerConfig attribute) ports (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) post() (nanobrain.library.infrastructure.interfaces.APIInterface method) (nanobrain.library.infrastructure.interfaces.external.APIInterface method) PostgreSQLAdapter (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.database) PostgreSQLConfig (class in nanobrain.library.infrastructure.interfaces.database) pre (nanobrain.core.config.schema_validator.ValidatorFunction attribute) preferred_format (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.StreamingChatRequest attribute) preferred_output_types (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.WorkflowRequirements attribute) prefix (nanobrain.library.interfaces.web.config.web_interface_config.APIConfig attribute) preload_workflows() (nanobrain.library.interfaces.web.servers.universal_server.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.servers.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.UniversalNanoBrainServer method) preserve_session_history (nanobrain.core.workflow.WorkflowProgress attribute) preview (nanobrain.library.interfaces.web.api.frontend_router.ConversationSummary attribute) primary_mode (nanobrain.core.config.enhanced_config.InputOutputFormat attribute) primary_name (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.TaxonInfo attribute) print_error() (nanobrain.library.infrastructure.BaseCLI method) (nanobrain.library.infrastructure.interfaces.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.base_cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.BaseCLI method) print_output() (nanobrain.library.infrastructure.BaseCLI method) (nanobrain.library.infrastructure.interfaces.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.base_cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.BaseCLI method) priority (nanobrain.library.agents.enhanced.delegation_engine.DelegationRule attribute) (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) (nanobrain.library.infrastructure.load_balancing.request_queue.QueuedRequest attribute) (nanobrain.library.infrastructure.steps.parallel_step.ProcessingRequest attribute) (nanobrain.library.infrastructure.steps.ProcessingRequest attribute) PROCEDURE_REQUEST (nanobrain.library.interfaces.web.IntentType attribute) (nanobrain.library.interfaces.web.models.IntentType attribute) (nanobrain.library.interfaces.web.models.universal_models.IntentType attribute) PROCESS (nanobrain.core.executor.ExecutorType attribute) process() (nanobrain.ConversationalAgent method) (nanobrain.core.Agent method), [1] (nanobrain.core.agent.Agent method) (nanobrain.core.agent.ConversationalAgent method) (nanobrain.core.agent.SimpleAgent method) (nanobrain.core.BaseStep method), [1] (nanobrain.core.ConversationalAgent method), [1] (nanobrain.core.guards.examples.protected_step_example.ProtectedStepExample method) (nanobrain.core.SimpleAgent method), [1] (nanobrain.core.Step method), [1] (nanobrain.core.step.BaseStep method) (nanobrain.core.step.Step method) (nanobrain.core.step.TransformStep method) (nanobrain.core.TransformStep method), [1] (nanobrain.core.Workflow method), [1] (nanobrain.core.workflow.Workflow method) (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent method) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent method) (nanobrain.library.agents.ConversationalSpecializedAgent method) (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent method) (nanobrain.library.agents.EnhancedCollaborativeAgent method) (nanobrain.library.agents.SimpleSpecializedAgent method) (nanobrain.library.agents.specialized.base.ConversationalSpecializedAgent method) (nanobrain.library.agents.specialized.base.SimpleSpecializedAgent method) (nanobrain.library.agents.specialized.ConversationalSpecializedAgent method) (nanobrain.library.agents.specialized.parsl_agent.ParslAgent method) (nanobrain.library.agents.specialized.ParslAgent method) (nanobrain.library.agents.specialized.SimpleSpecializedAgent method) (nanobrain.library.EnhancedCollaborativeAgent method), [1] (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStep method) (nanobrain.library.infrastructure.interfaces.cli.CLIStep method) (nanobrain.library.infrastructure.interfaces.CLIStep method) (nanobrain.library.infrastructure.ParallelStep method) (nanobrain.library.infrastructure.steps.parallel_step.ParallelStep method) (nanobrain.library.infrastructure.steps.ParallelStep method) (nanobrain.library.workflows.conversational.viral_expert_workflow.ViralExpertWorkflow method) (nanobrain.library.workflows.conversational.ViralExpertWorkflow method) (nanobrain.library.workflows.viral_protein_analysis.alphavirus_workflow.AlphavirusWorkflow method) (nanobrain.library.workflows.viral_protein_analysis.AlphavirusWorkflow method) (nanobrain.library.workflows.viral_protein_analysis.steps.alignment_step.AlignmentStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.AlignmentStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.annotation_mapping_step.AnnotationMappingStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.AnnotationMappingStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step.BVBRCDataAcquisitionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.BVBRCDataAcquisitionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.clustering_step.ClusteringStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.ClusteringStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step.BVBRCDataAcquisitionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_aggregation_step.DataAggregationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.DataAggregationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.EnhancedBVBRCDataAcquisitionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.protein_synonym_agent_step.ProteinSynonymAgentStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.ProteinSynonymAgentStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.pssm_analysis_step.PSSMAnalysisStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.PSSMAnalysisStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.result_collection_step.ResultCollectionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.ResultCollectionStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.sequence_curation_step.SequenceCurationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.SequenceCurationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.viral_pssm_generation_step.ViralPSSMGenerationStep method) (nanobrain.library.workflows.viral_protein_analysis.steps.ViralPSSMGenerationStep method) (nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow.ViralAnalysisWebWorkflow method) (nanobrain.library.workflows.viral_protein_analysis.web.ViralAnalysisWebWorkflow method) (nanobrain.Step method)

process_binary_content() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) process_biological_data() (nanobrain.core.bioinformatics.BioinformaticsTool method) (nanobrain.core.BioinformaticsTool method), [1] process_chat() (in module nanobrain.library.interfaces.web.api.chat_router) process_csv_content() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) process_generic_content() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) process_html_content() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) process_id (nanobrain.core.async_logging.LogMessage attribute) process_input() (nanobrain.library.infrastructure.interfaces.cli.command_processor.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.cli.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.CommandProcessor method) process_json_content() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) process_markdown_content() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) process_message() (nanobrain.library.workflows.ParslChatWorkflow method) process_messages_distributed() (nanobrain.library.workflows.ParslChatWorkflow method) process_response_content() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) process_sequences() (nanobrain.core.bioinformatics.BioinformaticsStep method) (nanobrain.core.BioinformaticsStep method), [1] process_text_content() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) process_universal_request() (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) process_user_input() (nanobrain.library.ChatWorkflow method), [1] (nanobrain.library.workflows.ChatWorkflow method) (nanobrain.library.workflows.ParslChatWorkflow method) process_with_tools() (nanobrain.core.Agent method), [1] (nanobrain.core.agent.Agent method) process_workflow_response() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) process_xml_content() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) ProcessExecutor (class in nanobrain.core), [1] (class in nanobrain.core.executor) processing_state (nanobrain.core.BaseStep attribute), [1] (nanobrain.core.step.BaseStep attribute) processing_time (nanobrain.library.infrastructure.steps.parallel_step.ProcessingResponse attribute) (nanobrain.library.infrastructure.steps.ProcessingResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.UniversalResponse attribute) (nanobrain.library.interfaces.web.UniversalResponse attribute) processing_time_ms (nanobrain.library.infrastructure.data.chat_session_data.ConversationalResponseData attribute) (nanobrain.library.infrastructure.data.chat_session_data.QueryClassificationData attribute) (nanobrain.library.infrastructure.data.ConversationalResponseData attribute) (nanobrain.library.infrastructure.data.QueryClassificationData attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.api.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.models.response_models.ChatMetadata attribute) ProcessingRequest (class in nanobrain.library.infrastructure.steps) (class in nanobrain.library.infrastructure.steps.parallel_step) ProcessingResponse (class in nanobrain.library.infrastructure.steps) (class in nanobrain.library.infrastructure.steps.parallel_step) processor_id (nanobrain.library.infrastructure.steps.parallel_step.ProcessingResponse attribute) (nanobrain.library.infrastructure.steps.ProcessingResponse attribute) processor_stats (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer attribute) (nanobrain.library.infrastructure.load_balancing.LoadBalancer attribute) (nanobrain.library.infrastructure.LoadBalancer attribute) ProcessorPool (class in nanobrain.library.infrastructure.steps) (class in nanobrain.library.infrastructure.steps.parallel_step) processors (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer attribute) (nanobrain.library.infrastructure.load_balancing.LoadBalancer attribute) (nanobrain.library.infrastructure.LoadBalancer attribute) ProcessSafeLogger (class in nanobrain.core.async_logging) progress (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.Workflow attribute) (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) PROGRESS (nanobrain.library.infrastructure.data.chat_session_data.MessageType attribute) (nanobrain.library.infrastructure.data.MessageType attribute) progress (nanobrain.library.interfaces.web.models.StreamingResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StreamingResponse attribute) (nanobrain.library.interfaces.web.StreamingResponse attribute) progress_batch_interval (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] progress_collapsed_by_default (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] progress_color (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) progress_config (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.processing.StreamingHandlerConfig attribute) progress_context() (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.cli.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.ProgressIndicator method) progress_info (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.StreamingChatResponse attribute) progress_percentage (nanobrain.core.workflow.ProgressStep attribute) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.AnalysisProgress attribute) progress_preserve_session_history (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] progress_show_technical_errors (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] progress_tracker (nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow.ViralAnalysisWebWorkflow attribute) (nanobrain.library.workflows.viral_protein_analysis.web.ViralAnalysisWebWorkflow attribute) PROGRESS_TRACKING (nanobrain.library.interfaces.web.InteractionPattern attribute) (nanobrain.library.interfaces.web.models.InteractionPattern attribute) (nanobrain.library.interfaces.web.models.workflow_models.InteractionPattern attribute) PROGRESS_UPDATE (nanobrain.library.interfaces.web.api.websocket_router.MessageType attribute) PROGRESS_UPDATES (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingType attribute) (nanobrain.library.interfaces.web.processing.StreamingType attribute) (nanobrain.library.interfaces.web.StreamingType attribute) ProgressConfig (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.cli) (class in nanobrain.library.infrastructure.interfaces.cli.progress_indicator) ProgressContext (class in nanobrain.library.infrastructure.interfaces.cli.progress_indicator) ProgressIndicator (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.cli) (class in nanobrain.library.infrastructure.interfaces.cli.progress_indicator) progressive_scaling (nanobrain.core.external_tool.ExternalToolConfig attribute) ProgressiveScalingMixin (class in nanobrain.core.progressive_scaling) ProgressReporter (class in nanobrain.core.workflow) ProgressStep (class in nanobrain.core.workflow) ProgressStyle (class in nanobrain.library.infrastructure.interfaces.cli.progress_indicator) prompt_manager (nanobrain.library.agents.specialized.protein_synonym_agent.ProteinSynonymAgent attribute) (nanobrain.library.agents.specialized.ProteinSynonymAgent attribute) prompt_prefix (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) prompt_suffix (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) prompt_template_file (nanobrain.AgentConfig attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] prompt_templates (nanobrain.AgentConfig attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] prompt_tokens (nanobrain.library.interfaces.web.models.response_models.ChatMetadata attribute) prompts (nanobrain.core.prompt_template_manager.PromptTemplateConfig attribute) (nanobrain.core.PromptTemplateConfig attribute), [1] PromptTemplate (class in nanobrain.core), [1] (class in nanobrain.core.prompt_template_manager) PromptTemplateConfig (class in nanobrain.core), [1] (class in nanobrain.core.prompt_template_manager) PromptTemplateManager (class in nanobrain.core), [1] (class in nanobrain.core.prompt_template_manager) protected_methods (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig attribute) ProtectedStepExample (class in nanobrain.core.guards.examples.protected_step_example) PROTEIN (nanobrain.core.bioinformatics.SequenceType attribute) (nanobrain.core.SequenceType attribute), [1] PROTEIN_ANALYSIS (nanobrain.library.interfaces.web.DomainType attribute) (nanobrain.library.interfaces.web.models.DomainType attribute) (nanobrain.library.interfaces.web.models.universal_models.DomainType attribute) PROTEIN_CHARS (nanobrain.core.sequence_manager.SequenceValidator attribute) (nanobrain.core.SequenceValidator attribute), [1] PROTEIN_SEQUENCE (nanobrain.library.interfaces.web.InputType attribute) (nanobrain.library.interfaces.web.models.InputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.InputType attribute) ProteinData (class in nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step) (class in nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step) ProteinSynonymAgent (class in nanobrain.library.agents.specialized) (class in nanobrain.library.agents.specialized.protein_synonym_agent) ProteinSynonymAgentStep (class in nanobrain.library.workflows.viral_protein_analysis.steps) (class in nanobrain.library.workflows.viral_protein_analysis.steps.protein_synonym_agent_step) protocol_performance (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) (nanobrain.library.EnhancedCollaborativeAgent attribute), [1] provider (nanobrain.core.a2a_support.A2AAgentCard attribute) (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.ToolCard attribute) ProviderConfig (class in nanobrain.core.config.config_manager) PSSMAnalysisStep (class in nanobrain.library.workflows.viral_protein_analysis.steps) (class in nanobrain.library.workflows.viral_protein_analysis.steps.pssm_analysis_step) publish() (nanobrain.library.infrastructure.interfaces.external.MessageQueueInterface method) (nanobrain.library.infrastructure.interfaces.MessageQueueInterface method) purpose (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.core.config.enhanced_config.AgentCardSection attribute) (nanobrain.core.config.enhanced_config.ToolCardSection attribute) push_notifications (nanobrain.core.card_schemas.AgentCapabilities attribute) (nanobrain.core.config.enhanced_config.A2ACapabilities attribute) pushNotifications (nanobrain.core.a2a_support.A2ACapabilities attribute) put() (nanobrain.library.infrastructure.load_balancing.request_queue.RequestQueue method) (nanobrain.library.infrastructure.load_balancing.RequestQueue method) (nanobrain.library.infrastructure.RequestQueue method)

Q

quality_analyzer (nanobrain.library.agents.specialized.code_writer.CodeWriterAgentMixin attribute) quality_controller (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.EnhancedBVBRCDataAcquisitionStep attribute) query (nanobrain.library.infrastructure.data.chat_session_data.ConversationalResponseData attribute) (nanobrain.library.infrastructure.data.ConversationalResponseData attribute) (nanobrain.library.interfaces.web.ChatRequest attribute) (nanobrain.library.interfaces.web.models.ChatRequest attribute) (nanobrain.library.interfaces.web.models.request_models.ChatRequest attribute) (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.StreamingChatRequest attribute) QueryAnalysisAgent (class in nanobrain.library.agents.specialized) (class in nanobrain.library.agents.specialized.query_analysis_agent)

QueryBuilder (class in nanobrain.library.infrastructure.interfaces.database) QueryClassificationData (class in nanobrain.library.infrastructure.data) (class in nanobrain.library.infrastructure.data.chat_session_data) QUESTION_ANSWER (nanobrain.library.interfaces.web.InteractionPattern attribute) (nanobrain.library.interfaces.web.models.InteractionPattern attribute) (nanobrain.library.interfaces.web.models.workflow_models.InteractionPattern attribute) QUEUE (nanobrain.core.link.LinkType attribute) (nanobrain.core.LinkType attribute), [1] QueuedRequest (class in nanobrain.library.infrastructure.load_balancing.request_queue) QueueLink (class in nanobrain.core), [1] (class in nanobrain.core.link)

R

RANDOM (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.load_balancing.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.steps.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.steps.parallel_step.LoadBalancingStrategy attribute) rate_limit (nanobrain.core.card_schemas.PerformanceMetrics attribute) (nanobrain.core.config.enhanced_config.PerformanceSpec attribute) rate_limit_per_minute (nanobrain.library.interfaces.web.config.web_interface_config.SecurityConfig attribute) rate_limiter (nanobrain.library.interfaces.web.web_interface.WebInterface attribute) (nanobrain.library.interfaces.web.WebInterface attribute) (nanobrain.library.interfaces.WebInterface attribute) rate_limiting (nanobrain.core.config.enhanced_config.ToolCapabilities attribute) raw_input (nanobrain.library.infrastructure.interfaces.cli.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.CLIContext attribute) read() (nanobrain.core.data_unit.DataUnitBase method) (nanobrain.core.DataUnitBase method), [1] (nanobrain.library.infrastructure.DataUnitBase method) read_file() (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin method) (nanobrain.library.infrastructure.interfaces.external.FileSystemInterface method) (nanobrain.library.infrastructure.interfaces.FileSystemInterface method) REAL_TIME_RESULTS (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingType attribute) (nanobrain.library.interfaces.web.processing.StreamingType attribute) (nanobrain.library.interfaces.web.StreamingType attribute) reasoning (nanobrain.library.infrastructure.data.chat_session_data.QueryClassificationData attribute) (nanobrain.library.infrastructure.data.QueryClassificationData attribute) receive() (nanobrain.library.infrastructure.interfaces.external.WebSocketInterface method) (nanobrain.library.infrastructure.interfaces.WebSocketInterface method) reconfigure_global_logging() (in module nanobrain.core.logging_system) record_annotation_result() (nanobrain.library.infrastructure.data.chat_session_data.InteractionMetrics method) record_custom_metric() (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor method) (nanobrain.library.infrastructure.PerformanceMonitor method) record_message() (nanobrain.library.infrastructure.data.chat_session_data.InteractionMetrics method) record_metric() (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor method) (nanobrain.library.infrastructure.PerformanceMonitor method) record_request() (nanobrain.library.infrastructure.data.email_manager.EmailManager method) (nanobrain.library.infrastructure.data.EmailManager method) record_request_end() (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer method) (nanobrain.library.infrastructure.load_balancing.LoadBalancer method) (nanobrain.library.infrastructure.LoadBalancer method) record_request_start() (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer method) (nanobrain.library.infrastructure.load_balancing.LoadBalancer method) (nanobrain.library.infrastructure.LoadBalancer method) redoc_url (nanobrain.library.interfaces.web.config.web_interface_config.APIConfig attribute) references (nanobrain.library.infrastructure.data.chat_session_data.ConversationalResponseData attribute) (nanobrain.library.infrastructure.data.ConversationalResponseData attribute) refresh_a2a_agents() (nanobrain.core.a2a_support.A2ASupportMixin method) refresh_mcp_tools() (nanobrain.core.mcp_support.MCPSupportMixin method) register() (nanobrain.core.config.component_factory.ComponentRegistry class method) (nanobrain.core.tool.ToolRegistry method) (nanobrain.core.ToolRegistry method), [1] register_agent_card() (nanobrain.core.card_schemas.CardManager method) register_change_listener() (nanobrain.core.data_unit.DataUnitBase method) (nanobrain.core.DataUnitBase method), [1] (nanobrain.library.infrastructure.DataUnitBase method) register_command() (nanobrain.library.infrastructure.BaseCLI method) (nanobrain.library.infrastructure.interfaces.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.base_cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.cli.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.CommandProcessor method) register_component() (in module nanobrain.core.logging_system) (nanobrain.core.logging_system.SystemLogManager method) register_input_data_unit() (nanobrain.core.BaseStep method), [1] (nanobrain.core.step.BaseStep method) register_output_data_unit() (nanobrain.core.BaseStep method), [1] (nanobrain.core.step.BaseStep method) register_tool() (nanobrain.core.Agent method), [1] (nanobrain.core.agent.Agent method) register_tool_card() (nanobrain.core.card_schemas.CardManager method) register_workflow_from_capabilities() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) register_workflow_from_config() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) registration_method (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.WorkflowRegistryEntry attribute) registration_timestamp (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.WorkflowRegistryEntry attribute) registry_maintenance (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.WorkflowRegistryConfig attribute) rejection_reason (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.ValidationResult attribute) release_connection() (nanobrain.library.infrastructure.interfaces.database.ConnectionPool method) reload (nanobrain.library.interfaces.web.config.web_interface_config.ServerConfig attribute) reload_config() (nanobrain.core.config.config_manager.ConfigManager method) remove_a2a_agent() (nanobrain.core.a2a_support.A2ASupportMixin method) remove_agent() (nanobrain.core.a2a_support.A2AClient method) remove_callback() (nanobrain.core.trigger.TriggerBase method) (nanobrain.core.TriggerBase method), [1] remove_container() (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase method) remove_delegation_rule() (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent method) remove_expired_requests() (nanobrain.library.infrastructure.load_balancing.request_queue.RequestQueue method) (nanobrain.library.infrastructure.load_balancing.RequestQueue method) (nanobrain.library.infrastructure.RequestQueue method) remove_guard_protection() (nanobrain.core.guards.nanobrain_guard_mixin.TriggerGuardMixin method) (nanobrain.core.guards.TriggerGuardMixin method) remove_job() (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData method) (nanobrain.library.infrastructure.data.ChatSessionData method) remove_link() (nanobrain.core.workflow.WorkflowGraph method) (nanobrain.core.WorkflowGraph method), [1] remove_mcp_server() (nanobrain.core.mcp_support.MCPSupportMixin method) remove_processor() (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer method) (nanobrain.library.infrastructure.load_balancing.LoadBalancer method) (nanobrain.library.infrastructure.LoadBalancer method) remove_progress() (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.cli.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.ProgressIndicator method) remove_rule() (nanobrain.library.agents.enhanced.delegation_engine.DelegationEngine method) remove_server() (nanobrain.core.mcp_support.MCPClient method) remove_step() (nanobrain.core.Workflow method), [1] (nanobrain.core.workflow.Workflow method) (nanobrain.core.workflow.WorkflowGraph method) (nanobrain.core.WorkflowGraph method), [1] replicas (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) REPORTS (nanobrain.library.interfaces.web.models.OutputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.OutputType attribute) (nanobrain.library.interfaces.web.OutputType attribute) representative_genomes (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.TaxonInfo attribute) request_data (nanobrain.library.infrastructure.load_balancing.request_queue.QueuedRequest attribute) request_id (nanobrain.core.ExecutionContext attribute), [1] (nanobrain.core.logging_system.ExecutionContext attribute) (nanobrain.library.infrastructure.load_balancing.request_queue.QueuedRequest attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.AgentResponse attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatResponse attribute) (nanobrain.library.infrastructure.steps.parallel_step.ProcessingResponse attribute) (nanobrain.library.infrastructure.steps.ProcessingResponse attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.api.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.ChatRequest attribute) (nanobrain.library.interfaces.web.ChatResponse attribute) (nanobrain.library.interfaces.web.ErrorResponse attribute) (nanobrain.library.interfaces.web.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.models.ChatRequest attribute) (nanobrain.library.interfaces.web.models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.ErrorResponse attribute) (nanobrain.library.interfaces.web.models.request_models.ChatRequest attribute) (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.models.response_models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.response_models.ErrorResponse attribute) (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.RequestAnalysis attribute) (nanobrain.library.interfaces.web.RequestAnalysis attribute) (nanobrain.library.interfaces.web.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.StreamingChatResponse attribute) request_timeout (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) RequestAnalysis (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.universal_models) RequestAnalyzerConfig (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.analysis) (class in nanobrain.library.interfaces.web.analysis.request_analyzer) RequestPriority (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.load_balancing) (class in nanobrain.library.infrastructure.load_balancing.request_queue) RequestQueue (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.load_balancing) (class in nanobrain.library.infrastructure.load_balancing.request_queue) require_connected_graph (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] require_natural_language_input (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.WorkflowRegistryConfig attribute) required (nanobrain.core.card_schemas.ParameterSchema attribute) REQUIRED (nanobrain.core.config.schema_validator.ConstraintType attribute) required (nanobrain.core.config.schema_validator.FieldSchema attribute) required_args (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) REQUIRED_CONFIG_FIELDS (nanobrain.core.Agent attribute), [1] (nanobrain.core.agent.Agent attribute) (nanobrain.core.BaseStep attribute), [1] (nanobrain.core.component_base.FromConfigBase attribute), [1] (nanobrain.core.ConditionalLink attribute), [1] (nanobrain.core.data_unit.DataUnitBase attribute) (nanobrain.core.DataUnitBase attribute), [1] (nanobrain.core.DirectLink attribute), [1] (nanobrain.core.executor.ExecutorBase attribute) (nanobrain.core.ExecutorBase attribute), [1] (nanobrain.core.external_tool.ExternalTool attribute) (nanobrain.core.FromConfigBase attribute), [1], [2], [3] (nanobrain.core.link.ConditionalLink attribute) (nanobrain.core.link.DirectLink attribute) (nanobrain.core.link.LinkBase attribute) (nanobrain.core.LinkBase attribute), [1] (nanobrain.core.Step attribute), [1] (nanobrain.core.step.BaseStep attribute) (nanobrain.core.step.Step attribute) (nanobrain.core.step.TransformStep attribute) (nanobrain.core.tool.ToolBase attribute) (nanobrain.core.ToolBase attribute), [1] (nanobrain.core.TransformStep attribute), [1] (nanobrain.core.trigger.TriggerBase attribute) (nanobrain.core.TriggerBase attribute), [1] (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.Workflow attribute) (nanobrain.DirectLink attribute) (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.ConversationalSpecializedAgent attribute) (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.SimpleSpecializedAgent attribute) (nanobrain.library.agents.specialized.base.BaseAgent attribute) (nanobrain.library.agents.specialized.base.ConversationalSpecializedAgent attribute) (nanobrain.library.agents.specialized.base.SimpleSpecializedAgent attribute) (nanobrain.library.agents.specialized.ConversationalSpecializedAgent attribute) (nanobrain.library.agents.specialized.SimpleSpecializedAgent attribute) (nanobrain.library.agents.specialized.virus_extraction_agent.VirusExtractionAgent attribute) (nanobrain.library.agents.specialized.VirusExtractionAgent attribute) (nanobrain.library.ChatWorkflow attribute), [1] (nanobrain.library.EnhancedCollaborativeAgent attribute), [1] (nanobrain.library.infrastructure.DataUnitBase attribute) (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase attribute) (nanobrain.library.infrastructure.docker.container_config.DockerComponentBase attribute) (nanobrain.library.interfaces.web.web_interface.WebInterface attribute) (nanobrain.library.interfaces.web.WebInterface attribute) (nanobrain.library.interfaces.WebInterface attribute) (nanobrain.library.workflows.ChatWorkflow attribute) (nanobrain.library.workflows.ParslChatWorkflow attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.annotation_mapping_step.AnnotationMappingStep attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.AnnotationMappingStep attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.data_aggregation_step.DataAggregationStep attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.DataAggregationStep attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.result_collection_step.ResultCollectionStep attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.ResultCollectionStep attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.viral_pssm_generation_step.ViralPSSMGenerationStep attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.ViralPSSMGenerationStep attribute) (nanobrain.Step attribute) required_domains (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.WorkflowRequirements attribute) required_fields (nanobrain.core.config.schema_validator.ConfigSchema attribute) required_input_types (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.WorkflowRequirements attribute) required_params (nanobrain.core.prompt_template_manager.PromptTemplate attribute) (nanobrain.core.PromptTemplate attribute), [1] requirements_metadata (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.models.WorkflowRequirements attribute) (nanobrain.library.interfaces.web.WorkflowRequirements attribute) reset() (nanobrain.library.infrastructure.CircuitBreaker method) (nanobrain.library.infrastructure.load_balancing.circuit_breaker.CircuitBreaker method) (nanobrain.library.infrastructure.load_balancing.CircuitBreaker method) reset_all_triggers() (in module nanobrain.core.guards) (in module nanobrain.core.guards.contextvar_core) reset_color (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute)

reset_statistics() (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent method) reset_stats() (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer method) (nanobrain.library.infrastructure.load_balancing.LoadBalancer method) (nanobrain.library.infrastructure.LoadBalancer method) resolution_stack (nanobrain.core.config.config_base.ConfigLoadingContext attribute) resolve_config_path() (in module nanobrain.core.a2a_support) (in module nanobrain.core.mcp_support) (nanobrain.core.ConfigLoader method), [1] (nanobrain.core.workflow.ConfigLoader method) resolve_dependencies() (nanobrain.core.AgentTool class method), [1] (nanobrain.core.AllDataReceivedTrigger class method), [1] (nanobrain.core.BaseStep class method), [1] (nanobrain.core.bioinformatics.BioinformaticsTool class method) (nanobrain.core.BioinformaticsTool class method), [1] (nanobrain.core.component_base.FromConfigBase class method) (nanobrain.core.ConditionalLink class method), [1] (nanobrain.core.data_unit.DataUnitBase class method) (nanobrain.core.data_unit.DataUnitFile class method) (nanobrain.core.data_unit.DataUnitString class method) (nanobrain.core.DataUnitBase class method), [1] (nanobrain.core.DataUnitFile class method), [1] (nanobrain.core.DataUnitString class method), [1] (nanobrain.core.DataUpdatedTrigger class method), [1] (nanobrain.core.DirectLink class method), [1] (nanobrain.core.executor.ExecutorBase class method) (nanobrain.core.ExecutorBase class method), [1] (nanobrain.core.external_tool.ExternalTool class method) (nanobrain.core.FromConfigBase class method), [1] (nanobrain.core.FunctionTool class method), [1] (nanobrain.core.LangChainTool class method), [1] (nanobrain.core.link.ConditionalLink class method) (nanobrain.core.link.DirectLink class method) (nanobrain.core.link.LinkBase class method) (nanobrain.core.LinkBase class method), [1] (nanobrain.core.mcp_support.MCPTool class method) (nanobrain.core.step.BaseStep class method) (nanobrain.core.step.TransformStep class method) (nanobrain.core.StepTool class method), [1] (nanobrain.core.TimerTrigger class method), [1] (nanobrain.core.tool.AgentTool class method) (nanobrain.core.tool.FunctionTool class method) (nanobrain.core.tool.LangChainTool class method) (nanobrain.core.tool.StepTool class method) (nanobrain.core.tool.ToolBase class method) (nanobrain.core.ToolBase class method), [1] (nanobrain.core.TransformStep class method), [1] (nanobrain.core.trigger.AllDataReceivedTrigger class method) (nanobrain.core.trigger.DataUnitChangeTrigger class method) (nanobrain.core.trigger.DataUpdatedTrigger class method) (nanobrain.core.trigger.TimerTrigger class method) (nanobrain.core.trigger.TriggerBase class method) (nanobrain.core.TriggerBase class method), [1] (nanobrain.DataUpdatedTrigger class method) (nanobrain.DirectLink class method) (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent class method) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent class method) (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent class method) (nanobrain.library.agents.EnhancedCollaborativeAgent class method) (nanobrain.library.agents.SimpleSpecializedAgent class method) (nanobrain.library.agents.specialized.base.SimpleSpecializedAgent class method) (nanobrain.library.agents.specialized.SimpleSpecializedAgent class method) (nanobrain.library.ChatWorkflow class method), [1] (nanobrain.library.EnhancedCollaborativeAgent class method), [1] (nanobrain.library.infrastructure.DataUnitBase class method) (nanobrain.library.infrastructure.DataUnitFile class method) (nanobrain.library.infrastructure.DataUnitString class method) (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase class method) (nanobrain.library.infrastructure.docker.container_config.DockerComponentBase class method) (nanobrain.library.interfaces.web.BaseUniversalServer class method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer class method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer class method) (nanobrain.library.interfaces.web.web_interface.WebInterface class method) (nanobrain.library.interfaces.web.WebInterface class method) (nanobrain.library.interfaces.WebInterface class method) (nanobrain.library.workflows.ChatWorkflow class method) resolve_link_endpoints() (nanobrain.core.link.LinkBase method) (nanobrain.core.LinkBase method), [1] resolve_virus_name() (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.VirusNameResolver method) resolved_references (nanobrain.core.config.config_base.ConfigBase attribute) (nanobrain.core.config.ConfigBase attribute) resource_allocation (nanobrain.library.interfaces.web.models.workflow_models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.WorkflowExecutionPlan attribute) resource_limits (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) resource_requirements (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) resource_usage (nanobrain.library.interfaces.web.models.response_models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.WorkflowStatusResponse attribute) ResourceLimits (class in nanobrain.library.infrastructure.docker.container_config) ResourceMonitor (class in nanobrain.core.resource_monitor) (class in nanobrain.library.infrastructure.monitoring) (class in nanobrain.library.infrastructure.monitoring.resource_monitor) ResourceMonitorConfig (class in nanobrain.core.resource_monitor) (class in nanobrain.library.infrastructure.monitoring) (class in nanobrain.library.infrastructure.monitoring.resource_monitor) ResourceNotification (class in nanobrain.core.resource_monitor) response (nanobrain.library.infrastructure.data.chat_session_data.ConversationalResponseData attribute) (nanobrain.library.infrastructure.data.ConversationalResponseData attribute) (nanobrain.library.infrastructure.steps.ChatResponse attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatResponse attribute) (nanobrain.library.interfaces.web.ChatResponse attribute) (nanobrain.library.interfaces.web.models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.response_models.ChatResponse attribute) response_format (nanobrain.library.interfaces.web.models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.StandardizedResponse attribute) response_id (nanobrain.library.interfaces.web.models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.UniversalResponse attribute) (nanobrain.library.interfaces.web.StandardizedResponse attribute) (nanobrain.library.interfaces.web.UniversalResponse attribute) response_length (nanobrain.core.agent_logging.AgentInteractionLog attribute) response_styles (nanobrain.core.card_schemas.AgentCard attribute) response_text (nanobrain.core.agent_logging.AgentInteractionLog attribute) (nanobrain.core.AgentConversationLog attribute), [1] (nanobrain.core.logging_system.AgentConversationLog attribute) response_time (nanobrain.library.infrastructure.data.chat_session_data.ConversationalResponseData attribute) (nanobrain.library.infrastructure.data.ConversationalResponseData attribute) response_time_ms (nanobrain.library.infrastructure.data.conversation_history.ConversationMessage attribute) (nanobrain.library.infrastructure.data.ConversationMessage attribute) response_timeout (nanobrain.library.infrastructure.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) response_type (nanobrain.library.infrastructure.data.chat_session_data.ConversationalResponseData attribute) (nanobrain.library.infrastructure.data.ConversationalResponseData attribute) (nanobrain.library.interfaces.web.models.universal_models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.UniversalResponse attribute) (nanobrain.library.interfaces.web.UniversalResponse attribute) response_validation (nanobrain.library.interfaces.web.processing.response_processor.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.ResponseProcessorConfig attribute) ResponseFormatter (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.cli) (class in nanobrain.library.infrastructure.interfaces.cli.response_formatter) ResponseProcessorConfig (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.processing) (class in nanobrain.library.interfaces.web.processing.response_processor) ResponseStatus (class in nanobrain.library.interfaces.web.models.response_models) restart_container() (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase method) restart_policy (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) RestartPolicy (class in nanobrain.library.infrastructure.docker.container_config) restore_all_methods() (nanobrain.core.guards.nanobrain_guard_mixin.TriggerGuardMixin method) (nanobrain.core.guards.TriggerGuardMixin method) restore_data_unit() (nanobrain.library.infrastructure.data.export_manager.ExportManager method) (nanobrain.library.infrastructure.data.ExportManager method) (nanobrain.library.infrastructure.ExportManager method) restore_from_checkpoint() (nanobrain.core.Workflow method), [1] (nanobrain.core.workflow.ProgressReporter method) (nanobrain.core.workflow.Workflow method) result (nanobrain.core.logging_system.ToolCallLog attribute) (nanobrain.core.ToolCallLog attribute), [1] (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) result_formatter (nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow.ViralAnalysisWebWorkflow attribute) (nanobrain.library.workflows.viral_protein_analysis.web.ViralAnalysisWebWorkflow attribute) ResultCollectionStep (class in nanobrain.library.workflows.viral_protein_analysis.steps) (class in nanobrain.library.workflows.viral_protein_analysis.steps.result_collection_step) results (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.AnalysisProgress attribute) retries (nanobrain.library.infrastructure.docker.container_config.HealthCheckConfig attribute) retrieve_sequence_regions() (nanobrain.core.bioinformatics.BioinformaticsDataUnit method) (nanobrain.core.BioinformaticsDataUnit method), [1] RETRY (nanobrain.core.ErrorHandlingStrategy attribute), [1] (nanobrain.core.workflow.ErrorHandlingStrategy attribute) retry_attempts (nanobrain.core.external_tool.ExternalToolConfig attribute) (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] (nanobrain.library.infrastructure.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) retry_delay (nanobrain.core.a2a_support.A2AAgentConfig attribute) (nanobrain.core.config.config_manager.ProviderConfig attribute) (nanobrain.core.mcp_support.MCPServerConfig attribute) (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) return_code (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.CommandResult attribute) returncode (nanobrain.core.external_tool.ToolResult attribute) RICH (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLITheme attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.OutputFormat attribute) RNA (nanobrain.core.bioinformatics.SequenceType attribute) (nanobrain.core.SequenceType attribute), [1] RNA_CHARS (nanobrain.core.sequence_manager.SequenceValidator attribute) (nanobrain.core.SequenceValidator attribute), [1] role (nanobrain.core.a2a_support.A2AMessage attribute) (nanobrain.library.infrastructure.data.chat_session_data.ChatMessage attribute) (nanobrain.library.infrastructure.data.ChatMessage attribute) ROLLBACK (nanobrain.core.ErrorHandlingStrategy attribute), [1] (nanobrain.core.workflow.ErrorHandlingStrategy attribute) ROUND_ROBIN (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.load_balancing.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.steps.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.steps.parallel_step.LoadBalancingStrategy attribute) route_best_match() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) route_confidence (nanobrain.library.interfaces.web.models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.models.universal_models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.models.universal_models.WorkflowRoute attribute) (nanobrain.library.interfaces.web.models.WorkflowRoute attribute) (nanobrain.library.interfaces.web.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.WorkflowRoute attribute) route_confidence_threshold() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) route_fallback_chain() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) route_id (nanobrain.library.interfaces.web.models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.models.universal_models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.models.universal_models.WorkflowRoute attribute) (nanobrain.library.interfaces.web.models.WorkflowRoute attribute) (nanobrain.library.interfaces.web.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.WorkflowRoute attribute) route_multi_workflow() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) route_request() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) routing_metadata (nanobrain.library.interfaces.web.models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.models.universal_models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.models.universal_models.WorkflowRoute attribute) (nanobrain.library.interfaces.web.models.WorkflowRoute attribute) (nanobrain.library.interfaces.web.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.WorkflowRoute attribute) routing_strategy (nanobrain.library.interfaces.web.models.universal_models.WorkflowRoute attribute) (nanobrain.library.interfaces.web.models.WorkflowRoute attribute) (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.WorkflowRoute attribute) (nanobrain.library.interfaces.web.WorkflowRouterConfig attribute) routing_strategy_config (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.WorkflowRouterConfig attribute) routing_thresholds (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.WorkflowRouterConfig attribute) RoutingStrategy (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.universal_models) RoutingStrategyConfig (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.routing) (class in nanobrain.library.interfaces.web.routing.routing_strategies) rule_based_config (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.IntentClassifierConfig attribute) rule_id (nanobrain.library.agents.enhanced.delegation_engine.DelegationRule attribute) run_demo_server() (in module nanobrain.library.interfaces.web.demo_server) run_phase5_validation() (in module nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration)

S

save_agent_card() (nanobrain.core.card_schemas.CardManager method) save_all_schemas() (nanobrain.core.config.schema_generator.SchemaGenerator method) save_config() (in module nanobrain.core.config.yaml_config) save_message() (nanobrain.library.ConversationHistoryUnit method), [1] (nanobrain.library.infrastructure.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.conversation_history.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.ConversationHistoryUnit method) save_schema() (nanobrain.core.config.schema_generator.SchemaGenerator method), [1] save_sequences_to_fasta() (nanobrain.core.sequence_manager.SequenceManager method) (nanobrain.core.SequenceManager method), [1] save_templates() (nanobrain.core.prompt_template_manager.PromptTemplateManager method) (nanobrain.core.PromptTemplateManager method), [1] save_to_yaml() (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig method) (nanobrain.library.interfaces.web.WebInterfaceConfig method) (nanobrain.library.interfaces.WebInterfaceConfig method) save_tool_card() (nanobrain.core.card_schemas.CardManager method) scaling_characteristics (nanobrain.core.card_schemas.PerformanceMetrics attribute) (nanobrain.core.config.enhanced_config.PerformanceSpec attribute) ScalingValidationMixin (class in nanobrain.core.progressive_scaling) scan_directory_for_workflows() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) schema (nanobrain.core.config.schema_validator.SchemaValidator attribute) (nanobrain.core.mcp_support.MCPToolInfo attribute) SchemaGenerator (class in nanobrain.core.config.schema_generator) SchemaValidator (class in nanobrain.core.config.schema_validator) schemes (nanobrain.core.a2a_support.A2AAuthentication attribute) scope (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig attribute) SCOPE_CONTEXT_VARS (nanobrain.core.guards.nanobrain_trigger_guard.NanobrainTriggerGuard attribute) (nanobrain.core.guards.NanobrainTriggerGuard attribute) scoring_metadata (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.WorkflowCompatibilityScore attribute) scoring_method (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.WorkflowCompatibilityScore attribute) scoring_weights (nanobrain.library.interfaces.web.routing.routing_strategies.RoutingStrategyConfig attribute) (nanobrain.library.interfaces.web.routing.RoutingStrategyConfig attribute) SCRIPT (nanobrain.library.infrastructure.interfaces.cli.command_processor.CommandType attribute) script_extensions (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) search_agents() (nanobrain.core.card_schemas.CardManager method) search_conversations() (nanobrain.library.ConversationHistoryUnit method), [1] (nanobrain.library.infrastructure.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.conversation_history.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.ConversationHistoryUnit method) search_term (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.CSVMatchCandidate attribute) search_tools() (nanobrain.core.card_schemas.CardManager method) security (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig attribute) (nanobrain.library.interfaces.web.WebInterfaceConfig attribute) (nanobrain.library.interfaces.WebInterfaceConfig attribute) security_context (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) security_manager (nanobrain.library.ChatWorkflow attribute), [1] (nanobrain.library.workflows.ChatWorkflow attribute) security_validator (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin attribute) SecurityConfig (class in nanobrain.library.interfaces.web.config.web_interface_config) select_processor() (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer method) (nanobrain.library.infrastructure.load_balancing.LoadBalancer method) (nanobrain.library.infrastructure.LoadBalancer method) select_workflow() (nanobrain.library.interfaces.web.AdaptiveStrategy method) (nanobrain.library.interfaces.web.BaseRoutingStrategy method) (nanobrain.library.interfaces.web.BestMatchStrategy method) (nanobrain.library.interfaces.web.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.BaseRoutingStrategy method) (nanobrain.library.interfaces.web.routing.BestMatchStrategy method) (nanobrain.library.interfaces.web.routing.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.BaseRoutingStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.BestMatchStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.MultiCriteriaStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.WeightedScoringStrategy method) (nanobrain.library.interfaces.web.routing.WeightedScoringStrategy method) (nanobrain.library.interfaces.web.WeightedScoringStrategy method) selected_workflow (nanobrain.library.interfaces.web.models.universal_models.WorkflowRoute attribute) (nanobrain.library.interfaces.web.models.WorkflowRoute attribute) (nanobrain.library.interfaces.web.WorkflowRoute attribute) semantic_config (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.DomainClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifierConfig attribute) (nanobrain.library.interfaces.web.analysis.IntentClassifierConfig attribute) send() (nanobrain.library.infrastructure.interfaces.external.WebSocketInterface method) (nanobrain.library.infrastructure.interfaces.WebSocketInterface method) send_chunk() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) send_error() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) send_progress_update() (in module nanobrain.library.interfaces.web.api.websocket_router) (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.WebSocketManager method) send_status_message() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) send_task() (nanobrain.core.a2a_support.A2AClient method) send_to_connection() (nanobrain.library.interfaces.web.api.websocket_router.ConnectionManager method) send_to_topic() (in module nanobrain.library.interfaces.web.api.websocket_router) (nanobrain.library.interfaces.web.api.websocket_router.ConnectionManager method) sequence_count (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineResult attribute) sequence_data (nanobrain.core.bioinformatics.SequenceRegion attribute) (nanobrain.core.SequenceRegion attribute), [1] sequence_id (nanobrain.core.bioinformatics.SequenceRegion attribute) (nanobrain.core.SequenceRegion attribute), [1] sequence_number (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.StreamingChatResponse attribute) sequence_type (nanobrain.core.bioinformatics.BioinformaticsConfig attribute) (nanobrain.core.bioinformatics.SequenceRegion attribute) (nanobrain.core.BioinformaticsConfig attribute), [1] (nanobrain.core.SequenceRegion attribute), [1] SequenceCoordinate (class in nanobrain.core), [1] (class in nanobrain.core.bioinformatics) SequenceCurationStep (class in nanobrain.library.workflows.viral_protein_analysis.steps) (class in nanobrain.library.workflows.viral_protein_analysis.steps.sequence_curation_step) SequenceData (class in nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step) (class in nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step) SequenceFormat (class in nanobrain.core), [1] (class in nanobrain.core.sequence_manager) SequenceManager (class in nanobrain.core), [1] (class in nanobrain.core.sequence_manager) SequenceRegion (class in nanobrain.core), [1] (class in nanobrain.core.bioinformatics) sequences_fasta (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineFiles attribute) SequenceStats (class in nanobrain.core), [1] (class in nanobrain.core.sequence_manager) SequenceType (class in nanobrain.core), [1] (class in nanobrain.core.bioinformatics) SequenceValidationError, [1], [2] SequenceValidator (class in nanobrain.core), [1] (class in nanobrain.core.sequence_manager) SEQUENTIAL (nanobrain.core.ExecutionStrategy attribute), [1] (nanobrain.core.workflow.ExecutionStrategy attribute) server (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig attribute) (nanobrain.library.interfaces.web.WebInterfaceConfig attribute) (nanobrain.library.interfaces.WebInterfaceConfig attribute) server_host (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneConfig attribute) server_instance (nanobrain.library.interfaces.web.web_interface.WebInterface attribute) (nanobrain.library.interfaces.web.WebInterface attribute) (nanobrain.library.interfaces.WebInterface attribute) server_name (nanobrain.core.mcp_support.MCPToolInfo attribute) server_port (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneConfig attribute) server_type (nanobrain.library.interfaces.web.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.base_server.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.BaseServerConfig attribute) (nanobrain.library.interfaces.web.servers.universal_server.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.servers.UniversalServerConfig attribute) server_type_mappings (nanobrain.library.interfaces.web.ServerFactoryConfig attribute) (nanobrain.library.interfaces.web.servers.server_factory.ServerFactoryConfig attribute) (nanobrain.library.interfaces.web.servers.ServerFactoryConfig attribute) server_url (nanobrain.core.mcp_support.MCPToolInfo attribute) ServerConfig (class in nanobrain.library.interfaces.web.config.web_interface_config) ServerFactoryConfig (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.servers) (class in nanobrain.library.interfaces.web.servers.server_factory) service_type (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) ServiceType (class in nanobrain.library.infrastructure.docker.container_config) session_duration (nanobrain.library.infrastructure.data.chat_session_data.InteractionMetrics attribute) session_id (nanobrain.core.workflow.WorkflowProgress attribute) (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData attribute) (nanobrain.library.infrastructure.data.ChatSessionData attribute) (nanobrain.library.infrastructure.data.session_manager.SessionData attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.CLIContext attribute) (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.StreamingChatResponse attribute) session_management (nanobrain.core.card_schemas.AgentCard attribute) session_timeout (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) SessionData (class in nanobrain.library.infrastructure.data.session_manager) sessionId (nanobrain.core.a2a_support.A2ATask attribute) SessionManager (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.data) (class in nanobrain.library.infrastructure.data.session_manager) set() (nanobrain.core.bioinformatics.BioinformaticsDataUnit method) (nanobrain.core.BioinformaticsDataUnit method), [1] (nanobrain.core.data_unit.DataUnit method) (nanobrain.core.data_unit.DataUnitBase method) (nanobrain.core.data_unit.DataUnitFile method) (nanobrain.core.data_unit.DataUnitMemory method) (nanobrain.core.data_unit.DataUnitStream method) (nanobrain.core.data_unit.DataUnitString method) (nanobrain.core.DataUnitBase method), [1] (nanobrain.core.DataUnitFile method), [1] (nanobrain.core.DataUnitMemory method), [1] (nanobrain.core.DataUnitStream method), [1] (nanobrain.core.DataUnitString method), [1] (nanobrain.DataUnitMemory method) (nanobrain.library.ConversationHistoryUnit method), [1] (nanobrain.library.DataUnitMemory method), [1] (nanobrain.library.infrastructure.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.conversation_history.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.ConversationHistoryUnit method) (nanobrain.library.infrastructure.data.export_manager.ExportManager method) (nanobrain.library.infrastructure.data.ExportManager method) (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.DataUnitBase method) (nanobrain.library.infrastructure.DataUnitFile method) (nanobrain.library.infrastructure.DataUnitMemory method) (nanobrain.library.infrastructure.DataUnitStream method) (nanobrain.library.infrastructure.DataUnitString method) (nanobrain.library.infrastructure.ExportManager method) (nanobrain.library.infrastructure.SessionManager method) set_a2a_config_path() (nanobrain.core.a2a_support.A2ASupportMixin method) set_color_scheme() (nanobrain.library.infrastructure.interfaces.cli.response_formatter.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.cli.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.ResponseFormatter method) set_debug_mode() (in module nanobrain.core), [1] (in module nanobrain.core.logging_system) set_format() (nanobrain.library.infrastructure.interfaces.cli.response_formatter.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.cli.ResponseFormatter method) (nanobrain.library.infrastructure.interfaces.ResponseFormatter method) set_input() (nanobrain.core.BaseStep method), [1] (nanobrain.core.step.BaseStep method) set_mcp_config_path() (nanobrain.core.mcp_support.MCPSupportMixin method) set_metadata() (nanobrain.core.data_unit.DataUnitBase method) (nanobrain.core.DataUnitBase method), [1] (nanobrain.library.infrastructure.DataUnitBase method) set_processor_weight() (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer method) (nanobrain.library.infrastructure.load_balancing.LoadBalancer method) (nanobrain.library.infrastructure.LoadBalancer method) set_provider_config() (nanobrain.core.config.config_manager.ConfigManager method) set_request_id() (nanobrain.library.interfaces.web.ChatRequest class method) (nanobrain.library.interfaces.web.models.ChatRequest class method) (nanobrain.library.interfaces.web.models.request_models.ChatRequest class method) (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest class method) (nanobrain.library.interfaces.web.models.StreamingChatRequest class method) (nanobrain.library.interfaces.web.StreamingChatRequest class method) set_scale_level() (nanobrain.core.progressive_scaling.ProgressiveScalingMixin method) set_session_data() (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.SessionManager method) set_session_id() (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest class method) (nanobrain.library.interfaces.web.models.StreamingChatRequest class method) (nanobrain.library.interfaces.web.StreamingChatRequest class method) set_user_notification_callback() (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitor method) (nanobrain.library.infrastructure.monitoring.ResourceMonitor method) setup_conda_environment() (nanobrain.core.bioinformatics.ExternalToolManager method) (nanobrain.core.ExternalToolManager method), [1] setup_cors() (in module nanobrain.library.interfaces.web.middleware) (in module nanobrain.library.interfaces.web.middleware.cors_middleware) setup_exception_handlers() (nanobrain.library.interfaces.web.servers.universal_server.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.servers.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.UniversalNanoBrainServer method) setup_factory_configuration() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory method) (nanobrain.library.interfaces.web.UniversalServerFactory method) setup_format_converters() (nanobrain.library.interfaces.web.FormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverter method) (nanobrain.library.interfaces.web.processing.FormatConverter method) setup_format_processors() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) setup_framework_integration() (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) setup_logging_integration() (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) setup_performance_optimizations() (nanobrain.library.interfaces.web.analysis.request_analyzer.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.analysis.UniversalRequestAnalyzer method) (nanobrain.library.interfaces.web.UniversalRequestAnalyzer method) setup_registry_configuration() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) setup_response_processing() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) setup_routing_configuration() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) setup_streaming_configuration() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) should_apply_guards() (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig method) (nanobrain.core.guards.NanobrainTriggerGuardConfig method) should_authenticate() (nanobrain.library.infrastructure.data.email_manager.EmailManager method) (nanobrain.library.infrastructure.data.EmailManager method) should_cache_response() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) should_delegate() (nanobrain.library.agents.enhanced.delegation_engine.DelegationEngine method) should_log_to_console() (in module nanobrain.core.config.config_manager) (nanobrain.core.config.config_manager.ConfigManager method) should_log_to_file() (in module nanobrain.core.config.config_manager) (nanobrain.core.config.config_manager.ConfigManager method) show_eta (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) show_percentage (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) show_progress() (in module nanobrain.library.infrastructure.interfaces.cli.progress_indicator) show_prompts (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) show_rate (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) show_stack_traces (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) show_technical_errors (nanobrain.core.workflow.WorkflowProgress attribute) show_timestamps (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) shutdown() (nanobrain.core.a2a_support.A2AClient method) (nanobrain.core.Agent method), [1] (nanobrain.core.agent.Agent method) (nanobrain.core.agent_logging.AgentLogger method) (nanobrain.core.async_logging.ProcessSafeLogger method) (nanobrain.core.BaseStep method), [1] (nanobrain.core.data_unit.DataUnitBase method) (nanobrain.core.DataUnitBase method), [1] (nanobrain.core.executor.ExecutorBase method) (nanobrain.core.executor.LocalExecutor method) (nanobrain.core.executor.ParslExecutor method) (nanobrain.core.executor.ProcessExecutor method) (nanobrain.core.executor.ThreadExecutor method) (nanobrain.core.ExecutorBase method), [1] (nanobrain.core.LocalExecutor method), [1] (nanobrain.core.mcp_support.MCPClient method) (nanobrain.core.ParslExecutor method), [1] (nanobrain.core.ProcessExecutor method), [1] (nanobrain.core.step.BaseStep method) (nanobrain.core.ThreadExecutor method), [1] (nanobrain.core.tool.ToolBase method) (nanobrain.core.ToolBase method), [1] (nanobrain.core.Workflow method), [1] (nanobrain.core.workflow.Workflow method) (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent method) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent method) (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent method) (nanobrain.library.agents.EnhancedCollaborativeAgent method) (nanobrain.library.agents.specialized.base.SpecializedAgentBase method), [1] (nanobrain.library.agents.specialized.parsl_agent.ParslAgent method) (nanobrain.library.agents.specialized.ParslAgent method) (nanobrain.library.agents.specialized.SpecializedAgentBase method), [1] (nanobrain.library.agents.SpecializedAgentBase method), [1] (nanobrain.library.ChatWorkflow method), [1] (nanobrain.library.EnhancedCollaborativeAgent method), [1] (nanobrain.library.infrastructure.BaseCLI method) (nanobrain.library.infrastructure.DataUnitBase method) (nanobrain.library.infrastructure.interfaces.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.base_cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStep method) (nanobrain.library.infrastructure.interfaces.cli.CLIStep method) (nanobrain.library.infrastructure.interfaces.CLIStep method) (nanobrain.library.infrastructure.ParallelAgentStep method) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentStep method) (nanobrain.library.infrastructure.steps.ParallelAgentStep method) (nanobrain.library.interfaces.web.chatbot_server.ChatbotServer method) (nanobrain.library.interfaces.web.web_interface.WebInterface method) (nanobrain.library.interfaces.web.WebInterface method) (nanobrain.library.interfaces.WebInterface method) (nanobrain.library.ParallelAgentStep method), [1] (nanobrain.library.workflows.ChatWorkflow method) (nanobrain.library.workflows.ParslChatWorkflow method) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneViralProteinInterface method) (nanobrain.LocalExecutor method) (nanobrain.ParslExecutor method) shutdown_a2a() (nanobrain.core.a2a_support.A2ASupportMixin method) shutdown_all() (nanobrain.core.async_logging.AsyncLoggerFactory class method) (nanobrain.core.tool.ToolRegistry method) (nanobrain.core.ToolRegistry method), [1] shutdown_all_loggers() (in module nanobrain.core.async_logging) shutdown_mcp() (nanobrain.core.mcp_support.MCPSupportMixin method) SimpleAgent (class in nanobrain.core), [1] (class in nanobrain.core.agent) SimpleSpecializedAgent (class in nanobrain.library.agents) (class in nanobrain.library.agents.specialized) (class in nanobrain.library.agents.specialized.base) SINGLE_COMMAND (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIMode attribute) size() (nanobrain.library.infrastructure.load_balancing.request_queue.RequestQueue method) (nanobrain.library.infrastructure.load_balancing.RequestQueue method) (nanobrain.library.infrastructure.RequestQueue method) Skill (class in nanobrain.core.card_schemas) skills (nanobrain.core.a2a_support.A2AAgentCard attribute) (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.config.enhanced_config.AgentCardSection attribute) SKIPPED (nanobrain.core.testing.test_constants.TestResult attribute) (nanobrain.core.testing.TestResult attribute) skipped_value (nanobrain.core.testing.test_result_config.TestResultConfig attribute) (nanobrain.core.testing.TestResultConfig attribute) source (nanobrain.core.link.LinkBase attribute) (nanobrain.core.link.LinkBase property) (nanobrain.core.LinkBase attribute), [1] (nanobrain.core.LinkBase property), [1]

source_responses (nanobrain.library.interfaces.web.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.AggregatedResponse attribute) source_url (nanobrain.core.card_schemas.ToolCard attribute) specialized_logger (nanobrain.library.agents.specialized.base.SpecializedAgentBase attribute) (nanobrain.library.agents.specialized.SpecializedAgentBase attribute) (nanobrain.library.agents.SpecializedAgentBase attribute) SpecializedAgentBase (class in nanobrain.library.agents) (class in nanobrain.library.agents.specialized) (class in nanobrain.library.agents.specialized.base) species_validation (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.CSVMatchCandidate attribute) species_validation_agent (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.EnhancedBVBRCDataAcquisitionStep attribute) SPINNER (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressStyle attribute) spinner_chars (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) spinner_interval (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) SQLInterface (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.database) SQLiteAdapter (class in nanobrain.library.infrastructure) (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.database) SQLiteConfig (class in nanobrain.library.infrastructure.interfaces.database) SQLQuery (class in nanobrain.library.infrastructure.interfaces.database) SQLQueryBuilder (class in nanobrain.library.infrastructure.interfaces.database) SQLResult (class in nanobrain.library.infrastructure.interfaces.database) stack_trace (nanobrain.library.interfaces.web.ErrorResponse attribute) (nanobrain.library.interfaces.web.models.ErrorResponse attribute) (nanobrain.library.interfaces.web.models.response_models.ErrorResponse attribute) StandaloneConfig (class in nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface) StandaloneViralProteinInterface (class in nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface) standardization (nanobrain.library.interfaces.web.processing.response_processor.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.ResponseProcessorConfig attribute) standardize_coordinates() (nanobrain.core.bioinformatics.BioinformaticsStep method) (nanobrain.core.BioinformaticsStep method), [1] standardize_response() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) StandardizedResponse (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.universal_models) start (nanobrain.core.bioinformatics.SequenceCoordinate attribute) (nanobrain.core.SequenceCoordinate attribute), [1] start() (nanobrain.core.ConditionalLink method), [1] (nanobrain.core.DirectLink method), [1] (nanobrain.core.FileLink method), [1] (nanobrain.core.link.ConditionalLink method) (nanobrain.core.link.DirectLink method) (nanobrain.core.link.FileLink method) (nanobrain.core.link.LinkBase method) (nanobrain.core.link.QueueLink method) (nanobrain.core.link.TransformLink method) (nanobrain.core.LinkBase method), [1] (nanobrain.core.QueueLink method), [1] (nanobrain.core.TransformLink method), [1] (nanobrain.DirectLink method) (nanobrain.library.infrastructure.BaseCLI method) (nanobrain.library.infrastructure.InteractiveCLI method) (nanobrain.library.infrastructure.interfaces.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.base_cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLI method) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLI method) (nanobrain.library.infrastructure.interfaces.InteractiveCLI method) (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.chatbot_server.ChatbotServer method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.universal_server.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.servers.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.UniversalNanoBrainServer method) start_container() (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase method) start_execution() (nanobrain.library.infrastructure.data.AnnotationJobData method) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData method) start_monitoring() (nanobrain.core.AllDataReceivedTrigger method), [1] (nanobrain.core.DataUpdatedTrigger method), [1] (nanobrain.core.ManualTrigger method), [1] (nanobrain.core.resource_monitor.ResourceMonitor method) (nanobrain.core.TimerTrigger method), [1] (nanobrain.core.trigger.AllDataReceivedTrigger method) (nanobrain.core.trigger.DataUnitChangeTrigger method) (nanobrain.core.trigger.DataUpdatedTrigger method) (nanobrain.core.trigger.ManualTrigger method) (nanobrain.core.trigger.TimerTrigger method) (nanobrain.core.trigger.TriggerBase method) (nanobrain.core.TriggerBase method), [1] (nanobrain.DataUpdatedTrigger method) (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitor method) (nanobrain.library.infrastructure.monitoring.ResourceMonitor method) (nanobrain.library.infrastructure.PerformanceMonitor method) start_period (nanobrain.library.infrastructure.docker.container_config.HealthCheckConfig attribute) start_server() (nanobrain.library.interfaces.web.web_interface.WebInterface method) (nanobrain.library.interfaces.web.WebInterface method) (nanobrain.library.interfaces.WebInterface method) start_time (nanobrain.core.ExecutionContext attribute), [1] (nanobrain.core.logging_system.ExecutionContext attribute) (nanobrain.core.workflow.ProgressStep attribute) (nanobrain.core.workflow.WorkflowProgress attribute) started_at (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) startup_config (nanobrain.library.interfaces.web.servers.universal_server.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.servers.UniversalServerConfig attribute) (nanobrain.library.interfaces.web.UniversalServerConfig attribute) startup_sequence() (nanobrain.library.interfaces.web.servers.universal_server.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.servers.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.UniversalNanoBrainServer method) state (nanobrain.core.a2a_support.A2ATaskStatus attribute) (nanobrain.library.infrastructure.CircuitBreaker attribute) (nanobrain.library.infrastructure.load_balancing.circuit_breaker.CircuitBreaker attribute) (nanobrain.library.infrastructure.load_balancing.CircuitBreaker attribute) state_transition_history (nanobrain.core.card_schemas.AgentCapabilities attribute) (nanobrain.core.config.enhanced_config.A2ACapabilities attribute) stateTransitionHistory (nanobrain.core.a2a_support.A2ACapabilities attribute) status (nanobrain.core.a2a_support.A2ATask attribute) (nanobrain.core.workflow.ProgressStep attribute) (nanobrain.core.workflow.WorkflowProgress attribute) (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.api.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.api.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.api.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.ChatResponse attribute) (nanobrain.library.interfaces.web.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.HealthResponse attribute) (nanobrain.library.interfaces.web.models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.HealthResponse attribute) (nanobrain.library.interfaces.web.models.response_models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.response_models.HealthResponse attribute) (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.response_models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.WorkflowStatusResponse attribute) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.AnalysisProgress attribute) STATUS_MESSAGES (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingType attribute) (nanobrain.library.interfaces.web.processing.StreamingType attribute) (nanobrain.library.interfaces.web.StreamingType attribute) STATUS_UPDATE (nanobrain.library.interfaces.web.api.websocket_router.MessageType attribute) StatusResponse (class in nanobrain.library.interfaces.web.models.response_models) stderr (nanobrain.core.external_tool.ToolResult attribute) (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.CommandResult attribute) stderr_text (nanobrain.core.external_tool.ToolResult property) stdout (nanobrain.core.external_tool.ToolResult attribute) (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.CommandResult attribute) stdout_text (nanobrain.core.external_tool.ToolResult property) Step (class in nanobrain) (class in nanobrain.core), [1] (class in nanobrain.core.step) STEP (nanobrain.core.tool.ToolType attribute) (nanobrain.core.ToolType attribute), [1] step_description (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIStepConfig attribute) STEP_EXECUTE (nanobrain.core.logging_system.OperationType attribute) (nanobrain.core.OperationType attribute), [1] step_id (nanobrain.core.workflow.ProgressStep attribute) step_name (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIStepConfig attribute) (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) step_registry (nanobrain.library.ChatWorkflow attribute), [1] (nanobrain.library.workflows.ChatWorkflow attribute) step_settings (nanobrain.library.infrastructure.interfaces.cli.cli_step.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIStepConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIStepConfig attribute) step_timeout (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] StepConfig (class in nanobrain) (class in nanobrain.core), [1] (class in nanobrain.core.step) steps (nanobrain.core.config.yaml_config.YAMLWorkflowConfig attribute) (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.Workflow attribute) (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.workflow.WorkflowProgress attribute) (nanobrain.core.WorkflowConfig attribute), [1] StepTool (class in nanobrain.core), [1] (class in nanobrain.core.tool) STOP (nanobrain.core.ErrorHandlingStrategy attribute), [1] (nanobrain.core.workflow.ErrorHandlingStrategy attribute) stop() (nanobrain.core.ConditionalLink method), [1] (nanobrain.core.DirectLink method), [1] (nanobrain.core.FileLink method), [1] (nanobrain.core.link.ConditionalLink method) (nanobrain.core.link.DirectLink method) (nanobrain.core.link.FileLink method) (nanobrain.core.link.LinkBase method) (nanobrain.core.link.QueueLink method) (nanobrain.core.link.TransformLink method) (nanobrain.core.LinkBase method), [1] (nanobrain.core.QueueLink method), [1] (nanobrain.core.TransformLink method), [1] (nanobrain.DirectLink method) (nanobrain.library.infrastructure.BaseCLI method) (nanobrain.library.infrastructure.interfaces.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.base_cli.BaseCLI method) (nanobrain.library.infrastructure.interfaces.cli.BaseCLI method) (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.universal_server.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.servers.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.UniversalNanoBrainServer method) stop_container() (nanobrain.library.infrastructure.docker.container_config.ContainerManagerBase method) stop_monitoring() (nanobrain.core.AllDataReceivedTrigger method), [1] (nanobrain.core.DataUpdatedTrigger method), [1] (nanobrain.core.ManualTrigger method), [1] (nanobrain.core.resource_monitor.ResourceMonitor method) (nanobrain.core.TimerTrigger method), [1] (nanobrain.core.trigger.AllDataReceivedTrigger method) (nanobrain.core.trigger.DataUnitChangeTrigger method) (nanobrain.core.trigger.DataUpdatedTrigger method) (nanobrain.core.trigger.ManualTrigger method) (nanobrain.core.trigger.TimerTrigger method) (nanobrain.core.trigger.TriggerBase method) (nanobrain.core.TriggerBase method), [1] (nanobrain.DataUpdatedTrigger method) (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.PerformanceMonitor method) (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitor method) (nanobrain.library.infrastructure.monitoring.ResourceMonitor method) (nanobrain.library.infrastructure.PerformanceMonitor method) store_bvbrc_result() (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusSpecificCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.VirusSpecificCacheManager method) store_ictv_standards() (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusSpecificCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.VirusSpecificCacheManager method) store_result() (nanobrain.library.workflows.viral_protein_analysis.base_cache_manager.BaseCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.BaseCacheManager method) store_sequence_regions() (nanobrain.core.bioinformatics.BioinformaticsDataUnit method) (nanobrain.core.BioinformaticsDataUnit method), [1] store_synonym_groups() (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusSpecificCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.VirusSpecificCacheManager method) store_virus_data() (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusSpecificCacheManager method) (nanobrain.library.workflows.viral_protein_analysis.VirusSpecificCacheManager method) strand (nanobrain.core.bioinformatics.SequenceCoordinate attribute) (nanobrain.core.SequenceCoordinate attribute), [1] strategy (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancer attribute) (nanobrain.library.infrastructure.load_balancing.LoadBalancer attribute) (nanobrain.library.infrastructure.LoadBalancer attribute) strategy_type (nanobrain.library.interfaces.web.routing.routing_strategies.RoutingStrategyConfig attribute) (nanobrain.library.interfaces.web.routing.RoutingStrategyConfig attribute) STREAM (nanobrain.core.card_schemas.InputMode attribute) (nanobrain.core.card_schemas.OutputMode attribute) stream_chat_response() (in module nanobrain.library.interfaces.web.api.websocket_router) stream_id (nanobrain.library.interfaces.web.models.StreamingResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StreamingResponse attribute) (nanobrain.library.interfaces.web.StreamingResponse attribute) stream_timeout (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.processing.StreamingHandlerConfig attribute) streaming (nanobrain.core.a2a_support.A2ACapabilities attribute) (nanobrain.core.card_schemas.AgentCapabilities attribute) (nanobrain.core.config.enhanced_config.A2ACapabilities attribute) (nanobrain.core.config.enhanced_config.ToolCapabilities attribute) STREAMING (nanobrain.library.interfaces.web.InteractionPattern attribute) (nanobrain.library.interfaces.web.models.InteractionPattern attribute) (nanobrain.library.interfaces.web.models.workflow_models.InteractionPattern attribute) streaming_config (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.StreamingChatRequest attribute) STREAMING_DATA (nanobrain.library.interfaces.web.models.OutputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.OutputType attribute) (nanobrain.library.interfaces.web.OutputType attribute) streaming_handler (nanobrain.library.interfaces.web.processing.response_processor.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.processing.ResponseProcessorConfig attribute) (nanobrain.library.interfaces.web.ResponseProcessorConfig attribute) streaming_metadata (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.StreamingChatResponse attribute) StreamingChatRequest (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.request_models) StreamingChatResponse (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.response_models) StreamingHandler (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.processing) (class in nanobrain.library.interfaces.web.processing.streaming_handler) StreamingHandlerConfig (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.processing) (class in nanobrain.library.interfaces.web.processing.streaming_handler) StreamingResponse (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.universal_models) StreamingType (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.processing) (class in nanobrain.library.interfaces.web.processing.streaming_handler) StreamSession (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.processing) (class in nanobrain.library.interfaces.web.processing.streaming_handler) strict_validation (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.WorkflowRegistryConfig attribute) STRING (nanobrain.core.card_schemas.ParameterType attribute) (nanobrain.core.config.schema_validator.FieldType attribute) STRUCTURED (nanobrain.core.card_schemas.OutputMode attribute) STRUCTURED_DATA (nanobrain.library.interfaces.web.InputType attribute) (nanobrain.library.interfaces.web.models.InputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.InputType attribute) STRUCTURED_INFORMATION (nanobrain.library.interfaces.web.models.OutputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.OutputType attribute) (nanobrain.library.interfaces.web.OutputType attribute) style (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) subcategory (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.core.config.enhanced_config.ToolCardSection attribute) submit() (nanobrain.core.executor.ParslExecutor method) (nanobrain.core.ParslExecutor method), [1] (nanobrain.ParslExecutor method) submit_message() (nanobrain.library.workflows.ParslChatWorkflow method) SUBMITTED (nanobrain.core.a2a_support.TaskStatus attribute) SUBSCRIBE (nanobrain.library.interfaces.web.api.websocket_router.MessageType attribute) subscribe() (nanobrain.core.data_unit.DataUnitStream method) (nanobrain.core.DataUnitStream method), [1] (nanobrain.library.infrastructure.DataUnitStream method) (nanobrain.library.infrastructure.interfaces.external.MessageQueueInterface method) (nanobrain.library.infrastructure.interfaces.MessageQueueInterface method) (nanobrain.library.interfaces.web.api.websocket_router.ConnectionManager method) success (nanobrain.core.agent_logging.AgentInteractionLog attribute) (nanobrain.core.ExecutionContext attribute), [1] (nanobrain.core.external_tool.ToolResult attribute) (nanobrain.core.logging_system.ExecutionContext attribute) SUCCESS (nanobrain.core.testing.test_constants.TestResult attribute) (nanobrain.core.testing.TestResult attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.MessageType attribute) success (nanobrain.library.infrastructure.steps.parallel_step.ProcessingResponse attribute) (nanobrain.library.infrastructure.steps.ProcessingResponse attribute) (nanobrain.library.interfaces.web.AggregatedResponse attribute) (nanobrain.library.interfaces.web.ChatResponse attribute) (nanobrain.library.interfaces.web.models.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.response_models.ChatResponse attribute) SUCCESS (nanobrain.library.interfaces.web.models.response_models.ResponseStatus attribute) success (nanobrain.library.interfaces.web.models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.models.WorkflowDiscoveryResult attribute) (nanobrain.library.interfaces.web.StandardizedResponse attribute) (nanobrain.library.interfaces.web.UniversalResponse attribute) (nanobrain.library.interfaces.web.WorkflowDiscoveryResult attribute) (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.CommandResult attribute) (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineResult attribute) success_threshold (nanobrain.library.infrastructure.docker.container_config.HealthCheckConfig attribute) success_value (nanobrain.core.testing.test_result_config.TestResultConfig attribute) (nanobrain.core.testing.TestResultConfig attribute) successful_annotations (nanobrain.library.infrastructure.data.chat_session_data.InteractionMetrics attribute) successful_delegations (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) (nanobrain.library.EnhancedCollaborativeAgent attribute), [1] suggest_fixes (nanobrain.core.external_tool.ExternalToolConfig attribute) suggest_similar_names() (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.VirusNameResolver method) suggested_fixes (nanobrain.core.external_tool.DiagnosticReport attribute) suggestions (nanobrain.core.external_tool.InstallationStatus attribute) supported_conversions (nanobrain.library.interfaces.web.processing.format_converter.FormatConverterConfig attribute) (nanobrain.library.interfaces.web.processing.FormatConverterConfig attribute) supported_features (nanobrain.library.interfaces.web.api.frontend_router.SystemInfo attribute) supported_formats (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin attribute) supported_languages (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.library.agents.specialized.code_writer.CodeWriterAgentMixin attribute) supported_modes (nanobrain.core.config.enhanced_config.InputOutputFormat attribute) supported_stream_types (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandlerConfig attribute) (nanobrain.library.interfaces.web.processing.StreamingHandlerConfig attribute) synonyms (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.TaxonInfo attribute) (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.TaxonResolution attribute) SYSTEM (nanobrain.library.infrastructure.data.chat_session_data.MessageRole attribute) (nanobrain.library.infrastructure.data.MessageRole attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CommandType attribute) system_prompt (nanobrain.AgentConfig attribute) (nanobrain.core.Agent attribute), [1] (nanobrain.core.agent.Agent attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.library.interfaces.web.ChatOptions attribute) (nanobrain.library.interfaces.web.models.ChatOptions attribute) (nanobrain.library.interfaces.web.models.request_models.ChatOptions attribute) system_requirements (nanobrain.core.card_schemas.ToolCard attribute) SystemInfo (class in nanobrain.library.interfaces.web.api.frontend_router) SystemLogManager (class in nanobrain.core.logging_system)

T

TABLE (nanobrain.library.infrastructure.interfaces.cli.response_formatter.OutputFormat attribute) table_border (nanobrain.library.infrastructure.interfaces.cli.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.FormatterConfig attribute) table_header (nanobrain.library.infrastructure.interfaces.cli.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.FormatterConfig attribute) tag (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) tags (nanobrain.core.a2a_support.A2ASkill attribute) (nanobrain.core.card_schemas.Skill attribute) (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.core.card_schemas.UsageExample attribute) (nanobrain.core.config.enhanced_config.ToolCardSection attribute) (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMetric attribute) target (nanobrain.core.link.LinkBase attribute) (nanobrain.core.link.LinkBase property) (nanobrain.core.LinkBase attribute), [1] (nanobrain.core.LinkBase property), [1] (nanobrain.library.agents.enhanced.delegation_engine.DelegationRule attribute) target_cpu_utilization (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) target_memory_utilization (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) target_type (nanobrain.library.agents.enhanced.delegation_engine.DelegationRule attribute) task_cache_ttl (nanobrain.core.a2a_support.A2AClientConfig attribute) TaskStatus (class in nanobrain.core.a2a_support) taxon_id (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineResult attribute) (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.TaxonInfo attribute) (nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver.TaxonResolution attribute) TaxonInfo (class in nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver) taxonomic_validation (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.CSVMatchCandidate attribute) taxonomic_validation_agent (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.EnhancedBVBRCDataAcquisitionStep attribute) TaxonResolution (class in nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver) team_sessions (nanobrain.library.agents.enhanced.collaborative_agent.CollaborativeAgent attribute) technical_details (nanobrain.core.workflow.ProgressStep attribute) temp_cache_dir() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestVirusSpecificCacheManagerInheritance method) temp_dir (nanobrain.core.bioinformatics.BioinformaticsConfig attribute) (nanobrain.core.BioinformaticsConfig attribute), [1] temperature (nanobrain.AgentConfig attribute) (nanobrain.core.Agent attribute), [1] (nanobrain.core.agent.Agent attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.library.interfaces.web.ChatOptions attribute) (nanobrain.library.interfaces.web.models.ChatOptions attribute) (nanobrain.library.interfaces.web.models.request_models.ChatOptions attribute) (nanobrain.library.interfaces.web.models.response_models.ChatMetadata attribute) template_system (nanobrain.library.agents.specialized.code_writer.CodeWriterAgentMixin attribute) (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin attribute) templates (nanobrain.library.infrastructure.interfaces.cli.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.response_formatter.FormatterConfig attribute) (nanobrain.library.infrastructure.interfaces.FormatterConfig attribute) terminate_stream() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamingHandler method) (nanobrain.library.interfaces.web.processing.StreamingHandler method) (nanobrain.library.interfaces.web.StreamingHandler method) test_a2a_support() (in module nanobrain.core.a2a_support) test_base_cache_manager_import() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestImportValidation method) test_base_cache_manager_is_abstract() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestBaseCacheManagerValidation method) test_base_cache_stats() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestCacheStats method) test_base_functionality_available() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestVirusSpecificCacheManagerInheritance method) test_bvbrc_cache_key_generation() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestBVBRCFunctionalityMigration method) test_bvbrc_cache_operations() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestBVBRCFunctionalityMigration method) test_bvbrc_migrated_functionality_available() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestVirusSpecificCacheManagerInheritance method) test_cache_identifier_implementation() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestVirusSpecificCacheManagerInheritance method) test_concrete_implementation_required() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestBaseCacheManagerValidation method) test_concrete_implementation_works() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestBaseCacheManagerValidation method) test_ictv_standards_operations() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestVirusSpecificOperations method) test_inheritance_structure() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestVirusSpecificCacheManagerInheritance method) test_mcp_support() (in module nanobrain.core.mcp_support) test_no_bvbrc_cache_manager_import() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestImportValidation method) test_package_exports() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestImportValidation method) test_rule() (nanobrain.library.agents.enhanced.delegation_engine.DelegationEngine method) test_synonym_groups_operations() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestVirusSpecificOperations method) test_virus_cache_directory_creation() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestVirusSpecificOperations method) test_virus_data_operations() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestVirusSpecificOperations method) test_virus_specific_cache_manager_import() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestImportValidation method) test_virus_specific_functionality_available() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestVirusSpecificCacheManagerInheritance method) test_virus_specific_stats() (nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration.TestCacheStats method) TestBaseCacheManagerValidation (class in nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration) TestBVBRCFunctionalityMigration (class in nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration) TestCacheStats (class in nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration) TestConstants (class in nanobrain.core.testing) (class in nanobrain.core.testing.test_constants) TestImportValidation (class in nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration) TestResult (class in nanobrain.core.testing) (class in nanobrain.core.testing.test_constants) TestResultConfig (class in nanobrain.core.testing) (class in nanobrain.core.testing.test_result_config) TestVirusSpecificCacheManagerInheritance (class in nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration) TestVirusSpecificOperations (class in nanobrain.library.workflows.viral_protein_analysis.test_phase5_cache_integration) text (nanobrain.core.a2a_support.A2APart attribute) TEXT (nanobrain.core.a2a_support.PartType attribute) (nanobrain.core.card_schemas.InputMode attribute) (nanobrain.core.card_schemas.OutputMode attribute) TextConverter (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.processing) (class in nanobrain.library.interfaces.web.processing.format_converter) theme (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) THREAD (nanobrain.core.executor.ExecutorType attribute) thread_id (nanobrain.core.async_logging.LogMessage attribute) ThreadExecutor (class in nanobrain.core), [1] (class in nanobrain.core.executor) thresholds (nanobrain.library.interfaces.web.routing.routing_strategies.RoutingStrategyConfig attribute) (nanobrain.library.interfaces.web.routing.RoutingStrategyConfig attribute) timeout (nanobrain.core.a2a_support.A2AAgentConfig attribute) (nanobrain.core.config.config_manager.ProviderConfig attribute) (nanobrain.core.config.enhanced_config.EnhancedToolConfig attribute) (nanobrain.core.executor.ExecutorBase attribute) (nanobrain.core.executor.ExecutorConfig attribute) (nanobrain.core.ExecutorBase attribute), [1] (nanobrain.core.ExecutorConfig attribute), [1] (nanobrain.core.mcp_support.MCPServerConfig attribute) (nanobrain.core.tool.ToolBase attribute) (nanobrain.core.tool.ToolConfig attribute) (nanobrain.core.ToolBase attribute), [1] (nanobrain.core.ToolConfig attribute), [1] (nanobrain.ExecutorConfig attribute) (nanobrain.library.infrastructure.CircuitBreaker attribute) (nanobrain.library.infrastructure.docker.container_config.HealthCheckConfig attribute) (nanobrain.library.infrastructure.load_balancing.circuit_breaker.CircuitBreaker attribute) (nanobrain.library.infrastructure.load_balancing.CircuitBreaker attribute) (nanobrain.library.infrastructure.steps.parallel_step.ProcessingRequest attribute) (nanobrain.library.infrastructure.steps.ProcessingRequest attribute) timeout_config (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneConfig attribute) timeout_hours (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.EEEVAnalysisRequest attribute) timeout_seconds (nanobrain.core.external_tool.ExternalToolConfig attribute) (nanobrain.library.infrastructure.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) TIMER (nanobrain.core.trigger.TriggerType attribute) (nanobrain.core.TriggerType attribute), [1] timer_interval_ms (nanobrain.core.trigger.TriggerConfig attribute) (nanobrain.core.TriggerConfig attribute), [1] (nanobrain.TriggerConfig attribute) TimerTrigger (class in nanobrain.core), [1] (class in nanobrain.core.trigger) timestamp (nanobrain.core.agent_logging.AgentInteractionLog attribute) (nanobrain.core.AgentConversationLog attribute), [1] (nanobrain.core.async_logging.LogMessage attribute) (nanobrain.core.logging_system.AgentConversationLog attribute) (nanobrain.core.logging_system.ToolCallLog attribute) (nanobrain.core.ToolCallLog attribute), [1] (nanobrain.library.infrastructure.data.chat_session_data.ChatMessage attribute) (nanobrain.library.infrastructure.data.ChatMessage attribute) (nanobrain.library.infrastructure.data.conversation_history.ConversationMessage attribute) (nanobrain.library.infrastructure.data.ConversationMessage attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.CLIContext attribute) (nanobrain.library.infrastructure.load_balancing.request_queue.QueuedRequest attribute) (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMetric attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.AgentRequest attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.AgentResponse attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatRequest attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatResponse attribute) (nanobrain.library.infrastructure.steps.parallel_step.ProcessingRequest attribute) (nanobrain.library.infrastructure.steps.parallel_step.ProcessingResponse attribute) (nanobrain.library.infrastructure.steps.ProcessingRequest attribute) (nanobrain.library.infrastructure.steps.ProcessingResponse attribute) (nanobrain.library.interfaces.web.AggregatedResponse attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.api.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.api.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.api.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.api.websocket_router.WebSocketMessage attribute) (nanobrain.library.interfaces.web.ChatResponse attribute) (nanobrain.library.interfaces.web.ErrorResponse attribute) (nanobrain.library.interfaces.web.FrontendChatResponse attribute) (nanobrain.library.interfaces.web.FrontendErrorResponse attribute) (nanobrain.library.interfaces.web.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.HealthResponse attribute) (nanobrain.library.interfaces.web.models.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.ErrorResponse attribute) (nanobrain.library.interfaces.web.models.HealthResponse attribute) (nanobrain.library.interfaces.web.models.response_models.ChatResponse attribute) (nanobrain.library.interfaces.web.models.response_models.ErrorResponse attribute) (nanobrain.library.interfaces.web.models.response_models.HealthResponse attribute) (nanobrain.library.interfaces.web.models.response_models.StatusResponse attribute) (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.response_models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.models.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.models.StreamingResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.AggregatedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StreamingResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.StreamingChatResponse attribute) (nanobrain.library.interfaces.web.StreamingResponse attribute) (nanobrain.library.interfaces.web.UniversalResponse attribute) (nanobrain.library.interfaces.web.WorkflowStatusResponse attribute) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.AnalysisProgress attribute) timestamp_field (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) title (nanobrain.library.interfaces.web.api.frontend_router.ConversationSummary attribute) (nanobrain.library.interfaces.web.config.web_interface_config.APIConfig attribute) (nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface.StandaloneConfig attribute) to_csv() (nanobrain.library.interfaces.web.JSONConverter method) (nanobrain.library.interfaces.web.processing.format_converter.JSONConverter method) (nanobrain.library.interfaces.web.processing.JSONConverter method) to_dict() (nanobrain.core.a2a_support.A2AAgentCard method) (nanobrain.core.a2a_support.A2AAgentConfig method) (nanobrain.core.a2a_support.A2AClientConfig method) (nanobrain.core.async_logging.LogMessage method) (nanobrain.core.bioinformatics.SequenceCoordinate method) (nanobrain.core.bioinformatics.SequenceRegion method) (nanobrain.core.card_schemas.AgentCapabilities method) (nanobrain.core.card_schemas.AgentCard method) (nanobrain.core.card_schemas.IOSchema method) (nanobrain.core.card_schemas.ParameterSchema method) (nanobrain.core.card_schemas.PerformanceMetrics method) (nanobrain.core.card_schemas.Skill method) (nanobrain.core.card_schemas.ToolCard method) (nanobrain.core.card_schemas.UsageExample method) (nanobrain.core.guards.nanobrain_guard_config.NanobrainTriggerGuardConfig method) (nanobrain.core.guards.NanobrainTriggerGuardConfig method) (nanobrain.core.mcp_support.MCPClientConfig method) (nanobrain.core.mcp_support.MCPServerConfig method) (nanobrain.core.SequenceCoordinate method), [1] (nanobrain.core.SequenceRegion method), [1] (nanobrain.core.workflow.ProgressStep method) (nanobrain.core.workflow.WorkflowProgress method) (nanobrain.library.infrastructure.steps.AgentRequest method) (nanobrain.library.infrastructure.steps.AgentResponse method) (nanobrain.library.infrastructure.steps.ChatRequest method) (nanobrain.library.infrastructure.steps.ChatResponse method) (nanobrain.library.infrastructure.steps.parallel_agent_step.AgentRequest method) (nanobrain.library.infrastructure.steps.parallel_agent_step.AgentResponse method) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatRequest method) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatResponse method) (nanobrain.library.infrastructure.steps.parallel_step.ProcessingRequest method) (nanobrain.library.infrastructure.steps.parallel_step.ProcessingResponse method) (nanobrain.library.infrastructure.steps.ProcessingRequest method) (nanobrain.library.infrastructure.steps.ProcessingResponse method) (nanobrain.library.interfaces.web.api.websocket_router.WebSocketMessage method) (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig method) (nanobrain.library.interfaces.web.CSVConverter method) (nanobrain.library.interfaces.web.JSONConverter method) (nanobrain.library.interfaces.web.processing.CSVConverter method) (nanobrain.library.interfaces.web.processing.format_converter.CSVConverter method) (nanobrain.library.interfaces.web.processing.format_converter.JSONConverter method) (nanobrain.library.interfaces.web.processing.JSONConverter method) (nanobrain.library.interfaces.web.WebInterfaceConfig method) (nanobrain.library.interfaces.WebInterfaceConfig method) (nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step.AnnotationData method) (nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step.GenomeData method) (nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step.ProteinData method) (nanobrain.library.workflows.viral_protein_analysis.steps.bv_brc_data_acquisition_step.SequenceData method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step.AnnotationData method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step.GenomeData method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step.ProteinData method) (nanobrain.library.workflows.viral_protein_analysis.steps.data_acquisition_step.SequenceData method)

to_docker_compose_format() (nanobrain.library.infrastructure.docker.container_config.ContainerConfig method) to_docker_format() (nanobrain.library.infrastructure.docker.container_config.ContainerConfig method) (nanobrain.library.infrastructure.docker.container_config.HealthCheckConfig method) (nanobrain.library.infrastructure.docker.container_config.ResourceLimits method) to_fasta() (nanobrain.core.bioinformatics.SequenceRegion method) (nanobrain.core.SequenceRegion method), [1] to_html() (nanobrain.library.interfaces.web.processing.format_converter.TextConverter method) (nanobrain.library.interfaces.web.processing.TextConverter method) (nanobrain.library.interfaces.web.TextConverter method) to_json() (nanobrain.library.interfaces.web.CSVConverter method) (nanobrain.library.interfaces.web.processing.CSVConverter method) (nanobrain.library.interfaces.web.processing.format_converter.CSVConverter method) (nanobrain.library.interfaces.web.processing.format_converter.TextConverter method) (nanobrain.library.interfaces.web.processing.TextConverter method) (nanobrain.library.interfaces.web.TextConverter method) to_kubernetes_deployment() (nanobrain.library.infrastructure.docker.container_config.ContainerConfig method) to_kubernetes_format() (nanobrain.library.infrastructure.docker.container_config.ResourceLimits method) to_kubernetes_probe() (nanobrain.library.infrastructure.docker.container_config.HealthCheckConfig method) to_kubernetes_service() (nanobrain.library.infrastructure.docker.container_config.ContainerConfig method) to_langchain_tool() (nanobrain.core.Agent method), [1] (nanobrain.core.agent.Agent method) (nanobrain.core.tool.ToolBase method) (nanobrain.core.ToolBase method), [1] to_markdown() (nanobrain.library.interfaces.web.processing.format_converter.TextConverter method) (nanobrain.library.interfaces.web.processing.TextConverter method) (nanobrain.library.interfaces.web.TextConverter method) to_one_based() (nanobrain.core.bioinformatics.SequenceCoordinate method) (nanobrain.core.SequenceCoordinate method), [1] to_string() (nanobrain.library.interfaces.web.CSVConverter method) (nanobrain.library.interfaces.web.JSONConverter method) (nanobrain.library.interfaces.web.processing.CSVConverter method) (nanobrain.library.interfaces.web.processing.format_converter.CSVConverter method) (nanobrain.library.interfaces.web.processing.format_converter.JSONConverter method) (nanobrain.library.interfaces.web.processing.JSONConverter method) to_table() (nanobrain.library.interfaces.web.CSVConverter method) (nanobrain.library.interfaces.web.JSONConverter method) (nanobrain.library.interfaces.web.processing.CSVConverter method) (nanobrain.library.interfaces.web.processing.format_converter.CSVConverter method) (nanobrain.library.interfaces.web.processing.format_converter.JSONConverter method) (nanobrain.library.interfaces.web.processing.JSONConverter method) to_xml() (nanobrain.library.interfaces.web.JSONConverter method) (nanobrain.library.interfaces.web.processing.format_converter.JSONConverter method) (nanobrain.library.interfaces.web.processing.JSONConverter method) to_yaml() (nanobrain.core.config.config_base.ConfigBase method) (nanobrain.core.config.ConfigBase method) (nanobrain.core.config.yaml_config.YAMLConfig method), [1] (nanobrain.core.config.YAMLConfig method), [1] to_zero_based() (nanobrain.core.bioinformatics.SequenceCoordinate method) (nanobrain.core.SequenceCoordinate method), [1] token_count (nanobrain.library.interfaces.web.models.response_models.ChatMetadata attribute) tokens_used (nanobrain.library.infrastructure.steps.ChatResponse attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatResponse attribute) tolerations (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) tool_cache_ttl (nanobrain.core.mcp_support.MCPClientConfig attribute) TOOL_CALL (nanobrain.core.logging_system.OperationType attribute) (nanobrain.core.OperationType attribute), [1] tool_calls (nanobrain.core.AgentConversationLog attribute), [1] (nanobrain.core.logging_system.AgentConversationLog attribute) tool_card (nanobrain.core.config.enhanced_config.EnhancedToolConfig attribute) (nanobrain.core.tool.ToolBase attribute) (nanobrain.core.tool.ToolConfig attribute) (nanobrain.core.ToolBase attribute), [1] (nanobrain.core.ToolConfig attribute), [1] (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingConfig attribute) tool_keywords (nanobrain.library.agents.conversational.enhanced_collaborative_agent.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.conversational.EnhancedCollaborativeAgent attribute) (nanobrain.library.agents.EnhancedCollaborativeAgent attribute) (nanobrain.library.EnhancedCollaborativeAgent attribute), [1] tool_name (nanobrain.core.external_tool.DiagnosticReport attribute) (nanobrain.core.external_tool.ExternalToolConfig attribute) (nanobrain.core.logging_system.ToolCallLog attribute) (nanobrain.core.ToolCallLog attribute), [1] tool_registry (nanobrain.core.Agent attribute), [1] (nanobrain.core.agent.Agent attribute) tool_type (nanobrain.core.config.enhanced_config.EnhancedToolConfig attribute) (nanobrain.core.tool.ToolBase attribute) (nanobrain.core.tool.ToolConfig attribute) (nanobrain.core.ToolBase attribute), [1] (nanobrain.core.ToolConfig attribute), [1] tool_usage (nanobrain.core.card_schemas.AgentCapabilities attribute) (nanobrain.core.config.enhanced_config.A2ACapabilities attribute) ToolBase (class in nanobrain.core), [1] (class in nanobrain.core.tool) ToolCallLog (class in nanobrain.core), [1] (class in nanobrain.core.logging_system) ToolCapabilities (class in nanobrain.core.config.enhanced_config) ToolCard (class in nanobrain.core.card_schemas) ToolCardSection (class in nanobrain.core.config.enhanced_config) ToolConfig (class in nanobrain.core), [1] (class in nanobrain.core.tool) ToolExecutionError ToolInstallationError ToolRegistry (class in nanobrain.core), [1] (class in nanobrain.core.tool) ToolResult (class in nanobrain.core.external_tool) tools (nanobrain.AgentConfig attribute) (nanobrain.core.Agent attribute), [1] (nanobrain.core.agent.Agent attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] (nanobrain.core.BaseStep attribute), [1] (nanobrain.core.step.BaseStep attribute) (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.StepConfig attribute) tools_config (nanobrain.core.config.enhanced_config.EnhancedAgentConfig attribute) tools_config_path (nanobrain.AgentConfig attribute) (nanobrain.core.agent.AgentConfig attribute) (nanobrain.core.AgentConfig attribute), [1] ToolType (class in nanobrain.core), [1] (class in nanobrain.core.tool) topic_area (nanobrain.library.infrastructure.data.chat_session_data.ConversationalResponseData attribute) (nanobrain.library.infrastructure.data.ConversationalResponseData attribute) total_bytes (nanobrain.core.resource_monitor.DiskSpaceInfo attribute) total_gb (nanobrain.core.resource_monitor.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.DiskSpaceInfo attribute) total_mb (nanobrain.library.infrastructure.monitoring.MemoryInfo attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.MemoryInfo attribute) total_messages (nanobrain.library.infrastructure.data.chat_session_data.InteractionMetrics attribute) total_response_time (nanobrain.library.infrastructure.data.chat_session_data.InteractionMetrics attribute) total_tokens (nanobrain.core.agent_logging.AgentInteractionLog attribute) (nanobrain.core.AgentConversationLog attribute), [1] (nanobrain.core.logging_system.AgentConversationLog attribute) (nanobrain.library.interfaces.web.models.response_models.ChatMetadata attribute) TRACE (nanobrain.core.logging_system.LogLevel attribute) (nanobrain.core.LogLevel attribute), [1] trace() (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] trace_function_calls() (in module nanobrain.core), [1] (in module nanobrain.core.logging_system) track_token_usage (nanobrain.library.infrastructure.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) transfer() (nanobrain.core.ConditionalLink method), [1] (nanobrain.core.DirectLink method), [1] (nanobrain.core.FileLink method), [1] (nanobrain.core.link.ConditionalLink method) (nanobrain.core.link.DirectLink method) (nanobrain.core.link.FileLink method) (nanobrain.core.link.LinkBase method) (nanobrain.core.link.QueueLink method) (nanobrain.core.link.TransformLink method) (nanobrain.core.LinkBase method), [1] (nanobrain.core.QueueLink method), [1] (nanobrain.core.TransformLink method), [1] (nanobrain.DirectLink method) transfer_count (nanobrain.core.link.LinkBase attribute) (nanobrain.core.link.LinkBase property) (nanobrain.core.LinkBase attribute), [1] (nanobrain.core.LinkBase property), [1] TRANSFORM (nanobrain.core.link.LinkType attribute) (nanobrain.core.LinkType attribute), [1] transform_function (nanobrain.core.link.LinkBase attribute) (nanobrain.core.link.LinkConfig attribute) (nanobrain.core.LinkBase attribute), [1] (nanobrain.core.LinkConfig attribute), [1] (nanobrain.LinkConfig attribute) TransformLink (class in nanobrain.core), [1] (class in nanobrain.core.link) TransformStep (class in nanobrain.core), [1] (class in nanobrain.core.step) translate_sequence() (nanobrain.core.sequence_manager.SequenceManager method) (nanobrain.core.SequenceManager method), [1] TREE (nanobrain.library.infrastructure.interfaces.cli.response_formatter.OutputFormat attribute) trigger() (nanobrain.core.trigger.TriggerBase method) (nanobrain.core.TriggerBase method), [1] TRIGGER_ACTIVATE (nanobrain.core.logging_system.OperationType attribute) (nanobrain.core.OperationType attribute), [1] trigger_config (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.StepConfig attribute) trigger_count (nanobrain.core.trigger.TriggerBase attribute) (nanobrain.core.TriggerBase attribute), [1] trigger_type (nanobrain.core.trigger.TriggerBase attribute) (nanobrain.core.trigger.TriggerConfig attribute) (nanobrain.core.TriggerBase attribute), [1] (nanobrain.core.TriggerConfig attribute), [1] (nanobrain.TriggerConfig attribute) TriggerBase (class in nanobrain.core), [1] (class in nanobrain.core.trigger) TriggerConfig (class in nanobrain) (class in nanobrain.core), [1] (class in nanobrain.core.trigger) TriggerGuardConfig (class in nanobrain.core.guards.nanobrain_trigger_guard) TriggerGuardIntegration (class in nanobrain.core.guards) (class in nanobrain.core.guards.trigger_integration) TriggerGuardMixin (class in nanobrain.core.guards) (class in nanobrain.core.guards.nanobrain_guard_mixin) triggers (nanobrain.core.BaseStep attribute), [1] (nanobrain.core.config.yaml_config.YAMLWorkflowConfig attribute) (nanobrain.core.step.BaseStep attribute) (nanobrain.core.step.StepConfig attribute) (nanobrain.core.StepConfig attribute), [1] (nanobrain.core.Workflow attribute), [1] (nanobrain.core.workflow.Workflow attribute) (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.library.infrastructure.steps.parallel_agent_step.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.parallel_step.ParallelProcessingConfig attribute) (nanobrain.library.infrastructure.steps.ParallelAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelConversationalAgentConfig attribute) (nanobrain.library.infrastructure.steps.ParallelProcessingConfig attribute) (nanobrain.StepConfig attribute) TriggerType (class in nanobrain.core), [1] (class in nanobrain.core.trigger) type (nanobrain.core.a2a_support.A2APart attribute) (nanobrain.core.card_schemas.ParameterSchema attribute) TYPE (nanobrain.core.config.schema_validator.ConstraintType attribute) type (nanobrain.library.infrastructure.docker.container_config.HealthCheckConfig attribute) (nanobrain.library.interfaces.web.api.websocket_router.WebSocketMessage attribute) typical_response_time (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.PerformanceMetrics attribute) (nanobrain.core.config.enhanced_config.PerformanceSpec attribute)

U

unbind_action() (nanobrain.core.trigger.DataUnitChangeTrigger method) unique_md5 (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineFiles attribute) unique_md5_count (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineResult attribute) unit (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMetric attribute) UniversalNanoBrainServer (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.servers) (class in nanobrain.library.interfaces.web.servers.universal_server) UniversalRequestAnalyzer (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.analysis) (class in nanobrain.library.interfaces.web.analysis.request_analyzer) UniversalResponse (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.universal_models) UniversalResponseProcessor (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.processing) (class in nanobrain.library.interfaces.web.processing.response_processor) UniversalServerConfig (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.servers) (class in nanobrain.library.interfaces.web.servers.universal_server) UniversalServerFactory (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.servers) (class in nanobrain.library.interfaces.web.servers.server_factory) UNKNOWN (nanobrain.core.a2a_support.TaskStatus attribute) (nanobrain.library.interfaces.web.DomainType attribute) (nanobrain.library.interfaces.web.IntentType attribute) (nanobrain.library.interfaces.web.models.DomainType attribute) (nanobrain.library.interfaces.web.models.IntentType attribute) (nanobrain.library.interfaces.web.models.universal_models.DomainType attribute) (nanobrain.library.interfaces.web.models.universal_models.IntentType attribute) UNLESS_STOPPED (nanobrain.library.infrastructure.docker.container_config.RestartPolicy attribute) unregister() (nanobrain.core.tool.ToolRegistry method) (nanobrain.core.ToolRegistry method), [1] unregister_change_listener() (nanobrain.core.data_unit.DataUnitBase method) (nanobrain.core.DataUnitBase method), [1] (nanobrain.library.infrastructure.DataUnitBase method) unregister_command() (nanobrain.library.infrastructure.interfaces.cli.command_processor.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.cli.CommandProcessor method) (nanobrain.library.infrastructure.interfaces.CommandProcessor method) UNSUBSCRIBE (nanobrain.library.interfaces.web.api.websocket_router.MessageType attribute) unsubscribe() (nanobrain.core.data_unit.DataUnitStream method) (nanobrain.core.DataUnitStream method), [1] (nanobrain.library.infrastructure.DataUnitStream method) (nanobrain.library.interfaces.web.api.websocket_router.ConnectionManager method) update() (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressContext method) update_activity() (nanobrain.library.interfaces.web.processing.streaming_handler.StreamSession method) (nanobrain.library.interfaces.web.processing.StreamSession method) (nanobrain.library.interfaces.web.StreamSession method) update_adaptation_context() (nanobrain.library.interfaces.web.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.AdaptiveStrategy method) update_content() (nanobrain.library.infrastructure.data.chat_session_data.ChatMessage method) (nanobrain.library.infrastructure.data.ChatMessage method) update_domain_patterns() (nanobrain.library.interfaces.web.analysis.domain_classifier.DomainClassifier method) (nanobrain.library.interfaces.web.analysis.DomainClassifier method) (nanobrain.library.interfaces.web.DomainClassifier method) update_from_dict() (nanobrain.core.config.config_base.ConfigBase method) (nanobrain.core.config.ConfigBase method) (nanobrain.core.config.yaml_config.YAMLConfig method) (nanobrain.core.config.YAMLConfig method) update_intent_patterns() (nanobrain.library.interfaces.web.analysis.intent_classifier.IntentClassifier method) (nanobrain.library.interfaces.web.analysis.IntentClassifier method) (nanobrain.library.interfaces.web.IntentClassifier method) update_interval (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) update_job_status() (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData method) (nanobrain.library.infrastructure.data.ChatSessionData method) update_last_message_content() (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData method) (nanobrain.library.infrastructure.data.ChatSessionData method) update_performance_feedback() (nanobrain.library.interfaces.web.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.AdaptiveStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.AdaptiveStrategy method) update_performance_history() (nanobrain.library.interfaces.web.BaseRoutingStrategy method) (nanobrain.library.interfaces.web.routing.BaseRoutingStrategy method) (nanobrain.library.interfaces.web.routing.routing_strategies.BaseRoutingStrategy method) update_processor_stats() (nanobrain.library.infrastructure.steps.parallel_step.ProcessorPool method) (nanobrain.library.infrastructure.steps.ProcessorPool method) update_progress() (nanobrain.core.workflow.ProgressReporter method) (nanobrain.library.infrastructure.data.AnnotationJobData method) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData method) (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.cli.ProgressIndicator method) (nanobrain.library.infrastructure.interfaces.ProgressIndicator method)

update_prompt() (nanobrain.core.prompt_template_manager.PromptTemplateManager method) (nanobrain.core.PromptTemplateManager method), [1] update_rule() (nanobrain.library.agents.enhanced.delegation_engine.DelegationEngine method) update_session() (nanobrain.library.infrastructure.data.session_manager.SessionManager method) (nanobrain.library.infrastructure.data.SessionManager method) (nanobrain.library.infrastructure.SessionManager method) update_session_duration() (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData method) (nanobrain.library.infrastructure.data.ChatSessionData method) update_step() (nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow.WebProgressTracker method) (nanobrain.library.workflows.viral_protein_analysis.web.WebProgressTracker method) update_step_progress() (nanobrain.core.workflow.WorkflowProgress method) uptime_seconds (nanobrain.library.interfaces.web.api.frontend_router.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.api.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.models.response_models.StatusResponse attribute) (nanobrain.library.interfaces.web.models.response_models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.WorkflowStatusResponse attribute) URGENT (nanobrain.library.infrastructure.load_balancing.request_queue.RequestPriority attribute) (nanobrain.library.infrastructure.load_balancing.RequestPriority attribute) (nanobrain.library.infrastructure.RequestPriority attribute) url (nanobrain.core.a2a_support.A2AAgentCard attribute) (nanobrain.core.a2a_support.A2AAgentConfig attribute) (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.config.enhanced_config.AgentCardSection attribute) (nanobrain.core.mcp_support.MCPServerConfig attribute) usage (nanobrain.library.infrastructure.interfaces.cli.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLICommand attribute) (nanobrain.library.infrastructure.interfaces.CLICommand attribute) usage_examples (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.core.config.enhanced_config.AgentCardSection attribute) (nanobrain.core.config.enhanced_config.ToolCardSection attribute) usage_percent (nanobrain.core.resource_monitor.DiskSpaceInfo attribute) usage_percentage (nanobrain.library.infrastructure.monitoring.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.MemoryInfo attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.MemoryInfo attribute) UsageExample (class in nanobrain.core.card_schemas) (class in nanobrain.core.config.enhanced_config) use_ictv_standards (nanobrain.library.agents.specialized.protein_synonym_agent.ProteinSynonymAgent attribute) (nanobrain.library.agents.specialized.ProteinSynonymAgent attribute) use_rag (nanobrain.library.interfaces.web.ChatOptions attribute) (nanobrain.library.interfaces.web.models.ChatOptions attribute) (nanobrain.library.interfaces.web.models.request_models.ChatOptions attribute) used_bytes (nanobrain.core.resource_monitor.DiskSpaceInfo attribute) used_gb (nanobrain.core.resource_monitor.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.DiskSpaceInfo attribute) used_mb (nanobrain.library.infrastructure.monitoring.MemoryInfo attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.MemoryInfo attribute) USER (nanobrain.library.infrastructure.data.chat_session_data.MessageRole attribute) (nanobrain.library.infrastructure.data.MessageRole attribute) user (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) USER (nanobrain.library.infrastructure.interfaces.cli.command_processor.CommandType attribute) user_id (nanobrain.library.infrastructure.data.session_manager.SessionData attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.CLIContext attribute) (nanobrain.library.infrastructure.steps.ChatRequest attribute) (nanobrain.library.infrastructure.steps.parallel_conversational_agent_step.ChatRequest attribute) (nanobrain.library.interfaces.web.ChatRequest attribute) (nanobrain.library.interfaces.web.models.ChatRequest attribute) (nanobrain.library.interfaces.web.models.request_models.ChatRequest attribute) (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.models.StreamingChatRequest attribute) (nanobrain.library.interfaces.web.StreamingChatRequest attribute) user_input (nanobrain.library.infrastructure.data.conversation_history.ConversationMessage attribute) (nanobrain.library.infrastructure.data.ConversationMessage attribute) user_notification_enabled (nanobrain.library.infrastructure.monitoring.resource_monitor.ResourceMonitorConfig attribute) (nanobrain.library.infrastructure.monitoring.ResourceMonitorConfig attribute) user_preferences (nanobrain.library.infrastructure.data.chat_session_data.ChatSessionData attribute) (nanobrain.library.infrastructure.data.ChatSessionData attribute) user_query (nanobrain.library.infrastructure.data.AnnotationJobData attribute) (nanobrain.library.infrastructure.data.chat_session_data.AnnotationJobData attribute) user_satisfaction_score (nanobrain.library.infrastructure.data.chat_session_data.InteractionMetrics attribute) username (nanobrain.library.infrastructure.interfaces.database.DatabaseConfig attribute)

V

valid_bases (nanobrain.core.sequence_manager.SequenceStats attribute) (nanobrain.core.SequenceStats attribute), [1] validate_a2a_compliance() (nanobrain.core.config.enhanced_config.EnhancedAgentConfig method), [1] (nanobrain.core.config.enhanced_config_manager.EnhancedConfigManager method) validate_all_scale_levels() (nanobrain.core.progressive_scaling.ProgressiveScalingMixin method) validate_and_extract_tool_card() (nanobrain.core.tool.ToolBase class method) (nanobrain.core.ToolBase class method), [1] validate_api_keys() (nanobrain.core.config.config_manager.ConfigManager method) validate_card_sections() (nanobrain.core.config.enhanced_config_manager.EnhancedConfigManager method) validate_chunk_type() (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse class method) (nanobrain.library.interfaces.web.models.StreamingChatResponse class method) (nanobrain.library.interfaces.web.StreamingChatResponse class method) validate_class_field() (nanobrain.core.data_unit.DataUnitConfig class method) (nanobrain.core.DataUnitConfig class method), [1] (nanobrain.DataUnitConfig class method) validate_client_capabilities() (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest class method) (nanobrain.library.interfaces.web.models.StreamingChatRequest class method) (nanobrain.library.interfaces.web.StreamingChatRequest class method) validate_component_config() (in module nanobrain.core.config.component_factory) validate_component_health() (nanobrain.library.interfaces.web.servers.universal_server.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.servers.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.UniversalNanoBrainServer method) validate_component_initialization() (nanobrain.library.interfaces.web.servers.universal_server.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.servers.UniversalNanoBrainServer method) (nanobrain.library.interfaces.web.UniversalNanoBrainServer method) validate_config() (nanobrain.core.config.schema_validator.SchemaValidator method) (nanobrain.library.interfaces.web.config.ConfigurationManager static method) validate_config_against_schema() (in module nanobrain.core.config.schema_generator) validate_config_file() (nanobrain.core.config.config_base.ConfigBase class method) (nanobrain.core.config.ConfigBase class method) validate_config_schema() (nanobrain.core.component_base.FromConfigBase class method) (nanobrain.core.FromConfigBase class method), [1] validate_config_usage() (in module nanobrain.core.component_base) validate_config_with_schema() (in module nanobrain.core.config.schema_validator) validate_configuration() (nanobrain.core.config.config_manager.ConfigManager method) (nanobrain.core.config.yaml_config.YAMLConfig method) (nanobrain.core.config.YAMLConfig method) (nanobrain.library.infrastructure.data.email_manager.EmailManager method) (nanobrain.library.infrastructure.data.EmailManager method) (nanobrain.library.workflows.viral_protein_analysis.steps.elasticsearch_indexing_step.ElasticsearchIndexingStep method) validate_configuration_status() (nanobrain.library.interfaces.web.models.response_models.WorkflowStatusResponse class method) (nanobrain.library.interfaces.web.models.WorkflowStatusResponse class method) (nanobrain.library.interfaces.web.WorkflowStatusResponse class method) validate_configurations() (in module nanobrain.core.config.enhanced_config_manager) validate_content_format() (nanobrain.library.interfaces.web.models.response_models.StreamingChatResponse class method) (nanobrain.library.interfaces.web.models.StreamingChatResponse class method) (nanobrain.library.interfaces.web.StreamingChatResponse class method) validate_conversation_id() (nanobrain.library.interfaces.web.ChatOptions class method) (nanobrain.library.interfaces.web.models.ChatOptions class method) (nanobrain.library.interfaces.web.models.request_models.ChatOptions class method) validate_conversion() (nanobrain.library.interfaces.web.BaseFormatConverter method) (nanobrain.library.interfaces.web.processing.BaseFormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.BaseFormatConverter method) validate_conversion_output() (nanobrain.library.interfaces.web.FormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverter method) (nanobrain.library.interfaces.web.processing.FormatConverter method) validate_coordinates() (nanobrain.core.bioinformatics.SequenceCoordinate class method) (nanobrain.core.SequenceCoordinate class method), [1] validate_end_after_start() (nanobrain.core.bioinformatics.SequenceCoordinate class method) (nanobrain.core.SequenceCoordinate class method), [1] validate_factory_configuration() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory method) (nanobrain.library.interfaces.web.UniversalServerFactory method) validate_framework_compliance() (nanobrain.library.interfaces.web.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.base_server.BaseUniversalServer method) (nanobrain.library.interfaces.web.servers.BaseUniversalServer method) validate_graph (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] validate_graph() (nanobrain.core.workflow.WorkflowGraph method) (nanobrain.core.WorkflowGraph method), [1] validate_input() (nanobrain.library.interfaces.web.FormatConverter method) (nanobrain.library.interfaces.web.processing.format_converter.FormatConverter method) (nanobrain.library.interfaces.web.processing.FormatConverter method) validate_parameters() (nanobrain.core.config.schema_validator.SchemaValidator method) validate_preferred_format() (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest class method) (nanobrain.library.interfaces.web.models.StreamingChatRequest class method) (nanobrain.library.interfaces.web.StreamingChatRequest class method) validate_processing_configuration() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) validate_query() (nanobrain.library.interfaces.web.ChatRequest class method) (nanobrain.library.interfaces.web.models.ChatRequest class method) (nanobrain.library.interfaces.web.models.request_models.ChatRequest class method) (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest class method) (nanobrain.library.interfaces.web.models.StreamingChatRequest class method) (nanobrain.library.interfaces.web.StreamingChatRequest class method) validate_references() (nanobrain.core.config.yaml_config.YAMLWorkflowConfig method) validate_response() (nanobrain.library.interfaces.web.processing.response_processor.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.processing.UniversalResponseProcessor method) (nanobrain.library.interfaces.web.UniversalResponseProcessor method) validate_scale_configuration() (nanobrain.core.progressive_scaling.ScalingValidationMixin method) validate_sequence() (nanobrain.core.sequence_manager.SequenceValidator method) (nanobrain.core.SequenceValidator method), [1] validate_server_class_path() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory method) (nanobrain.library.interfaces.web.UniversalServerFactory method) validate_server_configuration() (nanobrain.library.interfaces.web.servers.server_factory.UniversalServerFactory method) (nanobrain.library.interfaces.web.servers.UniversalServerFactory method) (nanobrain.library.interfaces.web.UniversalServerFactory method) validate_status() (nanobrain.library.interfaces.web.models.response_models.WorkflowStatusResponse class method) (nanobrain.library.interfaces.web.models.WorkflowStatusResponse class method) (nanobrain.library.interfaces.web.WorkflowStatusResponse class method)

validate_streaming_config() (nanobrain.library.interfaces.web.models.request_models.StreamingChatRequest class method) (nanobrain.library.interfaces.web.models.StreamingChatRequest class method) (nanobrain.library.interfaces.web.StreamingChatRequest class method) validate_system_prompt() (nanobrain.library.interfaces.web.ChatOptions class method) (nanobrain.library.interfaces.web.models.ChatOptions class method) (nanobrain.library.interfaces.web.models.request_models.ChatOptions class method) validate_templates() (nanobrain.core.prompt_template_manager.PromptTemplateManager method) (nanobrain.core.PromptTemplateManager method), [1] validate_tool_card() (nanobrain.core.config.enhanced_config.EnhancedToolConfig method) validate_workflow_capabilities() (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistry method) (nanobrain.library.interfaces.web.routing.WorkflowRegistry method) (nanobrain.library.interfaces.web.WorkflowRegistry method) validation (nanobrain.core.config.enhanced_config.EnhancedAgentConfig attribute) validation_cache (nanobrain.core.config.schema_validator.SchemaValidator attribute) validation_checks (nanobrain.library.interfaces.web.models.workflow_models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.WorkflowValidationResult attribute) validation_details (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.ValidationResult attribute) validation_enabled (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.WorkflowRegistryConfig attribute) validation_errors (nanobrain.library.infrastructure.interfaces.cli.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.cli.command_processor.CLIContext attribute) (nanobrain.library.infrastructure.interfaces.CLIContext attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.WorkflowValidationResult attribute) validation_metadata (nanobrain.library.interfaces.web.models.workflow_models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.WorkflowValidationResult attribute) validation_method (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.ValidationResult attribute) validation_pipeline (nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step.EnhancedBVBRCDataAcquisitionStep attribute) validation_result (nanobrain.library.interfaces.web.models.workflow_models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.models.WorkflowRegistryEntry attribute) (nanobrain.library.interfaces.web.WorkflowRegistryEntry attribute) validation_timeout (nanobrain.library.interfaces.web.routing.workflow_registry.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRegistryConfig attribute) (nanobrain.library.interfaces.web.WorkflowRegistryConfig attribute) validation_warnings (nanobrain.library.interfaces.web.models.workflow_models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.WorkflowValidationResult attribute) ValidationResult (class in nanobrain.library.workflows.viral_protein_analysis.steps.enhanced_bv_brc_data_acquisition_step) ValidatorFunction (class in nanobrain.core.config.schema_validator) validators (nanobrain.core.config.schema_validator.ConfigSchema attribute) (nanobrain.core.config.schema_validator.SchemaValidator attribute) value (nanobrain.core.config.schema_validator.FieldConstraint attribute) (nanobrain.library.infrastructure.monitoring.performance_monitor.PerformanceMetric attribute) verify_installation() (nanobrain.core.external_tool.ExternalTool method) verify_on_init (nanobrain.core.external_tool.ExternalToolConfig attribute) version (nanobrain.core.a2a_support.A2AAgentCard attribute) (nanobrain.core.card_schemas.AgentCard attribute) (nanobrain.core.card_schemas.ToolCard attribute) (nanobrain.core.config.enhanced_config.AgentCardSection attribute) (nanobrain.core.config.enhanced_config.ToolCardSection attribute) (nanobrain.core.config.schema_validator.ConfigSchema attribute) (nanobrain.core.config.yaml_config.YAMLWorkflowConfig attribute) (nanobrain.core.external_tool.InstallationStatus attribute) (nanobrain.core.prompt_template_manager.PromptTemplateConfig attribute) (nanobrain.core.PromptTemplateConfig attribute), [1] (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) (nanobrain.library.interfaces.web.api.frontend_router.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.api.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.config.web_interface_config.APIConfig attribute) (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig attribute) (nanobrain.library.interfaces.web.FrontendHealthResponse attribute) (nanobrain.library.interfaces.web.HealthResponse attribute) (nanobrain.library.interfaces.web.models.HealthResponse attribute) (nanobrain.library.interfaces.web.models.response_models.HealthResponse attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WebInterfaceConfig attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) (nanobrain.library.interfaces.WebInterfaceConfig attribute) via_trigger() (in module nanobrain.core.guards) (in module nanobrain.core.guards.contextvar_core) (nanobrain.core.guards.nanobrain_trigger_guard.NanobrainTriggerGuard method) (nanobrain.core.guards.NanobrainTriggerGuard method) ViralAnalysisWebWorkflow (class in nanobrain.library.workflows.viral_protein_analysis.web) (class in nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow) ViralExpertWorkflow (class in nanobrain.library.workflows.conversational) (class in nanobrain.library.workflows.conversational.viral_expert_workflow) ViralPSSMGenerationStep (class in nanobrain.library.workflows.viral_protein_analysis.steps) (class in nanobrain.library.workflows.viral_protein_analysis.steps.viral_pssm_generation_step) VIROLOGY (nanobrain.library.interfaces.web.DomainType attribute) (nanobrain.library.interfaces.web.models.DomainType attribute) (nanobrain.library.interfaces.web.models.universal_models.DomainType attribute) VIRUS_NAME (nanobrain.library.interfaces.web.InputType attribute) (nanobrain.library.interfaces.web.models.InputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.InputType attribute) virus_species (nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager.VirusCacheEntry attribute) VirusCacheEntry (class in nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager) VirusExtractionAgent (class in nanobrain.library.agents.specialized) (class in nanobrain.library.agents.specialized.virus_extraction_agent) VirusNameResolver (class in nanobrain.library.workflows.viral_protein_analysis.virus_name_resolver) VirusSpecificCacheManager (class in nanobrain.library.workflows.viral_protein_analysis) (class in nanobrain.library.workflows.viral_protein_analysis.virus_specific_cache_manager) VISUALIZATIONS (nanobrain.library.interfaces.web.models.OutputType attribute) (nanobrain.library.interfaces.web.models.workflow_models.OutputType attribute) (nanobrain.library.interfaces.web.OutputType attribute) volumes (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute)

W

wait_for_workflow_completion() (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouter method) (nanobrain.library.interfaces.web.routing.WorkflowRouter method) (nanobrain.library.interfaces.web.WorkflowRouter method) warm_cache() (nanobrain.library.infrastructure.data.cache_manager.CacheManager method) (nanobrain.library.infrastructure.data.CacheManager method) WARNING (nanobrain.core.logging_system.LogLevel attribute) (nanobrain.core.LogLevel attribute), [1] (nanobrain.library.infrastructure.interfaces.cli.response_formatter.MessageType attribute) warning() (nanobrain.core.async_logging.ProcessSafeLogger method) (nanobrain.core.logging_system.NanoBrainLogger method) (nanobrain.core.NanoBrainLogger method), [1] warning_prefix (nanobrain.library.infrastructure.interfaces.cli.base_cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.CLIConfig attribute) (nanobrain.library.infrastructure.interfaces.CLIConfig attribute) warning_triggered (nanobrain.core.resource_monitor.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.MemoryInfo attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.DiskSpaceInfo attribute) (nanobrain.library.infrastructure.monitoring.resource_monitor.MemoryInfo attribute) warnings (nanobrain.library.interfaces.web.models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.StandardizedResponse attribute) (nanobrain.library.interfaces.web.StandardizedResponse attribute) web_config (nanobrain.library.interfaces.web.web_interface.WebInterface attribute) (nanobrain.library.interfaces.web.WebInterface attribute) (nanobrain.library.interfaces.WebInterface attribute) WebInterface (class in nanobrain.library.interfaces) (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.web_interface) WebInterfaceConfig (class in nanobrain.library.interfaces) (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.config.web_interface_config) WebProgressTracker (class in nanobrain.library.workflows.viral_protein_analysis.web) (class in nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow) WebResultFormatter (class in nanobrain.library.workflows.viral_protein_analysis.web) (class in nanobrain.library.workflows.viral_protein_analysis.web.viral_analysis_web_workflow) website (nanobrain.core.a2a_support.A2AProvider attribute) websocket_endpoint() (in module nanobrain.library.interfaces.web.api.websocket_router) websocket_manager (nanobrain.library.interfaces.web.web_interface.WebInterface attribute) (nanobrain.library.interfaces.web.WebInterface attribute) (nanobrain.library.interfaces.WebInterface attribute) websocket_url (nanobrain.library.interfaces.web.api.frontend_router.SystemInfo attribute) WebSocketInterface (class in nanobrain.library.infrastructure.interfaces) (class in nanobrain.library.infrastructure.interfaces.external) WebSocketManager (class in nanobrain.library.workflows.viral_protein_analysis.web.standalone_interface) WebSocketMessage (class in nanobrain.library.interfaces.web.api.websocket_router) WEIGHTED (nanobrain.library.infrastructure.steps.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.steps.parallel_step.LoadBalancingStrategy attribute) WEIGHTED_ROUND_ROBIN (nanobrain.library.infrastructure.load_balancing.load_balancer.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.load_balancing.LoadBalancingStrategy attribute) (nanobrain.library.infrastructure.LoadBalancingStrategy attribute) WeightedScoringStrategy (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.routing) (class in nanobrain.library.interfaces.web.routing.routing_strategies) welcome_message (nanobrain.library.infrastructure.interfaces.cli.interactive_cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.InteractiveCLIConfig attribute) (nanobrain.library.infrastructure.interfaces.InteractiveCLIConfig attribute) width (nanobrain.library.infrastructure.interfaces.cli.progress_indicator.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.cli.ProgressConfig attribute) (nanobrain.library.infrastructure.interfaces.ProgressConfig attribute) with_a2a_support() (in module nanobrain.core.a2a_support) with_mcp_support() (in module nanobrain.core.mcp_support) worker_pool (nanobrain.core.executor.ExecutorBase attribute) (nanobrain.core.ExecutorBase attribute), [1] workers (nanobrain.library.interfaces.web.config.web_interface_config.ServerConfig attribute) Workflow (class in nanobrain.core), [1] (class in nanobrain.core.workflow) workflow_class (nanobrain.library.interfaces.web.models.universal_models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowMatch attribute) workflow_config (nanobrain.library.ChatWorkflow attribute), [1] (nanobrain.library.workflows.ChatWorkflow attribute) workflow_config_path (nanobrain.library.interfaces.web.config.web_interface_config.WebInterfaceConfig attribute) (nanobrain.library.interfaces.web.WebInterfaceConfig attribute) (nanobrain.library.interfaces.WebInterfaceConfig attribute) workflow_directory (nanobrain.core.config.config_base.ConfigLoadingContext attribute) (nanobrain.core.workflow.WorkflowConfig attribute) (nanobrain.core.WorkflowConfig attribute), [1] workflow_id (nanobrain.core.workflow.WorkflowProgress attribute) (nanobrain.library.interfaces.web.models.response_models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.universal_models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.models.UniversalResponse attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.models.WorkflowMatch attribute) (nanobrain.library.interfaces.web.models.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.models.WorkflowValidationResult attribute) (nanobrain.library.interfaces.web.UniversalResponse attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCompatibilityScore attribute) (nanobrain.library.interfaces.web.WorkflowMatch attribute) (nanobrain.library.interfaces.web.WorkflowStatusResponse attribute) (nanobrain.library.interfaces.web.WorkflowValidationResult attribute)

workflow_integrator (nanobrain.library.agents.specialized.code_writer.CodeWriterAgentMixin attribute) workflow_metadata (nanobrain.library.interfaces.web.models.response_models.ChatMetadata attribute) workflow_name (nanobrain.core.workflow.WorkflowProgress attribute) (nanobrain.library.interfaces.web.models.workflow_models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.models.WorkflowCapabilities attribute) (nanobrain.library.interfaces.web.WorkflowCapabilities attribute) workflow_registry (nanobrain.library.interfaces.web.routing.workflow_router.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.routing.WorkflowRouterConfig attribute) (nanobrain.library.interfaces.web.WorkflowRouterConfig attribute) WORKFLOW_RUN (nanobrain.core.logging_system.OperationType attribute) (nanobrain.core.OperationType attribute), [1] workflow_sequence (nanobrain.library.interfaces.web.models.workflow_models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.models.WorkflowExecutionPlan attribute) (nanobrain.library.interfaces.web.WorkflowExecutionPlan attribute) workflow_status (nanobrain.library.interfaces.web.models.response_models.StatusResponse attribute) workflow_websocket() (in module nanobrain.library.interfaces.web.api.websocket_router) WorkflowCapabilities (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.workflow_models) WorkflowCompatibilityScore (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.workflow_models) WorkflowConfig (class in nanobrain.core), [1] (class in nanobrain.core.workflow) (in module nanobrain.core.config) WorkflowDiscoveryResult (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.workflow_models) WorkflowExecutionPlan (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.workflow_models) WorkflowGraph (class in nanobrain.core), [1] (class in nanobrain.core.workflow) WorkflowMatch (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.universal_models) WorkflowProgress (class in nanobrain.core.workflow) WorkflowRegistry (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.routing) (class in nanobrain.library.interfaces.web.routing.workflow_registry) WorkflowRegistryConfig (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.routing) (class in nanobrain.library.interfaces.web.routing.workflow_registry) WorkflowRegistryEntry (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.workflow_models) WorkflowRequirements (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.workflow_models) WorkflowRoute (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.universal_models) WorkflowRouter (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.routing) (class in nanobrain.library.interfaces.web.routing.workflow_router) WorkflowRouterConfig (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.routing) (class in nanobrain.library.interfaces.web.routing.workflow_router) workflows (nanobrain.library.interfaces.web.models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.models.universal_models.MultiWorkflowRoute attribute) (nanobrain.library.interfaces.web.MultiWorkflowRoute attribute) WorkflowStatusResponse (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.response_models) WorkflowValidationResult (class in nanobrain.library.interfaces.web) (class in nanobrain.library.interfaces.web.models) (class in nanobrain.library.interfaces.web.models.workflow_models) WORKING (nanobrain.core.a2a_support.TaskStatus attribute) working_dir (nanobrain.library.infrastructure.docker.container_config.ContainerConfig attribute) (nanobrain.library.workflows.viral_protein_analysis.bvbrc_command_pipeline.PipelineFiles attribute) wrap_trigger_execution() (nanobrain.core.guards.trigger_integration.TriggerGuardIntegration static method) (nanobrain.core.guards.TriggerGuardIntegration static method) write() (nanobrain.core.data_unit.DataUnitBase method) (nanobrain.core.DataUnitBase method), [1] (nanobrain.library.infrastructure.DataUnitBase method) write_code_to_file() (nanobrain.library.agents.specialized.code_writer.CodeWriterAgentMixin method) write_fasta_file() (nanobrain.core.FastaParser method), [1] (nanobrain.core.sequence_manager.FastaParser method) write_fasta_string() (nanobrain.core.FastaParser method), [1] (nanobrain.core.sequence_manager.FastaParser method) write_file() (nanobrain.library.agents.specialized.file_writer.FileWriterAgentMixin method) (nanobrain.library.infrastructure.interfaces.external.FileSystemInterface method) (nanobrain.library.infrastructure.interfaces.FileSystemInterface method)

Y

YAMLConfig (class in nanobrain.core.config) (class in nanobrain.core.config.yaml_config)

YAMLWorkflowConfig (class in nanobrain.core.config.yaml_config)

Z

ZERO_BASED (nanobrain.core.bioinformatics.CoordinateSystem attribute) (nanobrain.core.CoordinateSystem attribute), [1]